[1] "ofn"        "-oTLIHC-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LIHC-TP/22506983/LIHC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/22623049/transformed.cor.cli.txt"

nPatients in clinical file=377, in cluster file=373, common to both=373
[1] "Reduce the number of clustering variables from 100 to 99."
[1]  99 373
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           114            259 
  TP53 MUTATED TP53 WILD-TYPE 
           114            259 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              97              276 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              97              276 
[1] "AXIN1 MUTATION ANALYSIS"
[1] 3
  AXIN1 MUTATED AXIN1 WILD-TYPE 
             24             349 
  AXIN1 MUTATED AXIN1 WILD-TYPE 
             24             349 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           21           352 
  RB1 MUTATED RB1 WILD-TYPE 
           21           352 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              32              341 
  ARID1A MUTATED ARID1A WILD-TYPE 
              32              341 
[1] "BAP1 MUTATION ANALYSIS"
[1] 3
  BAP1 MUTATED BAP1 WILD-TYPE 
            21            352 
  BAP1 MUTATED BAP1 WILD-TYPE 
            21            352 
[1] "CDC27 MUTATION ANALYSIS"
[1] 3
  CDC27 MUTATED CDC27 WILD-TYPE 
             15             358 
  CDC27 MUTATED CDC27 WILD-TYPE 
             15             358 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              11              362 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              11              362 
[1] "KRT2 MUTATION ANALYSIS"
[1] 3
  KRT2 MUTATED KRT2 WILD-TYPE 
            12            361 
  KRT2 MUTATED KRT2 WILD-TYPE 
            12            361 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              13              360 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              13              360 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            11            362 
  PTEN MUTATED PTEN WILD-TYPE 
            11            362 
[1] "ARID2 MUTATION ANALYSIS"
[1] 3
  ARID2 MUTATED ARID2 WILD-TYPE 
             22             351 
  ARID2 MUTATED ARID2 WILD-TYPE 
             22             351 
[1] "RBM10 MUTATION ANALYSIS"
[1] 3
  RBM10 MUTATED RBM10 WILD-TYPE 
              8             365 
  RBM10 MUTATED RBM10 WILD-TYPE 
              8             365 
[1] "ZNF512B MUTATION ANALYSIS"
[1] 3
  ZNF512B MUTATED ZNF512B WILD-TYPE 
                8               365 
  ZNF512B MUTATED ZNF512B WILD-TYPE 
                8               365 
[1] "KCNN3 MUTATION ANALYSIS"
[1] 3
  KCNN3 MUTATED KCNN3 WILD-TYPE 
             12             361 
  KCNN3 MUTATED KCNN3 WILD-TYPE 
             12             361 
[1] "KRT10 MUTATION ANALYSIS"
[1] 3
  KRT10 MUTATED KRT10 WILD-TYPE 
              9             364 
  KRT10 MUTATED KRT10 WILD-TYPE 
              9             364 
[1] "APOB MUTATION ANALYSIS"
[1] 3
  APOB MUTATED APOB WILD-TYPE 
            39            334 
  APOB MUTATED APOB WILD-TYPE 
            39            334 
[1] "MLL4 MUTATION ANALYSIS"
[1] 3
  MLL4 MUTATED MLL4 WILD-TYPE 
            19            354 
  MLL4 MUTATED MLL4 WILD-TYPE 
            19            354 
[1] "ALB MUTATION ANALYSIS"
[1] 3
  ALB MUTATED ALB WILD-TYPE 
           43           330 
  ALB MUTATED ALB WILD-TYPE 
           43           330 
[1] "TSC2 MUTATION ANALYSIS"
[1] 3
  TSC2 MUTATED TSC2 WILD-TYPE 
            12            361 
  TSC2 MUTATED TSC2 WILD-TYPE 
            12            361 
[1] "IL6ST MUTATION ANALYSIS"
[1] 3
  IL6ST MUTATED IL6ST WILD-TYPE 
             12             361 
  IL6ST MUTATED IL6ST WILD-TYPE 
             12             361 
[1] "C19ORF55 MUTATION ANALYSIS"
[1] 3
  C19ORF55 MUTATED C19ORF55 WILD-TYPE 
                 6                367 
  C19ORF55 MUTATED C19ORF55 WILD-TYPE 
                 6                367 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              13              360 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              13              360 
[1] "CELA1 MUTATION ANALYSIS"
[1] 3
  CELA1 MUTATED CELA1 WILD-TYPE 
              6             367 
  CELA1 MUTATED CELA1 WILD-TYPE 
              6             367 
[1] "RPS6KA3 MUTATION ANALYSIS"
[1] 3
  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
               14               359 
  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
               14               359 
[1] "NRD1 MUTATION ANALYSIS"
[1] 3
  NRD1 MUTATED NRD1 WILD-TYPE 
            13            360 
  NRD1 MUTATED NRD1 WILD-TYPE 
            13            360 
[1] "EEF1A1 MUTATION ANALYSIS"
[1] 3
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
               9              364 
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
               9              364 
[1] "TCHH MUTATION ANALYSIS"
[1] 3
  TCHH MUTATED TCHH WILD-TYPE 
            17            356 
  TCHH MUTATED TCHH WILD-TYPE 
            17            356 
[1] "COG2 MUTATION ANALYSIS"
[1] 3
  COG2 MUTATED COG2 WILD-TYPE 
             4            369 
  COG2 MUTATED COG2 WILD-TYPE 
             4            369 
[1] "ATXN1 MUTATION ANALYSIS"
[1] 3
  ATXN1 MUTATED ATXN1 WILD-TYPE 
             10             363 
  ATXN1 MUTATED ATXN1 WILD-TYPE 
             10             363 
[1] "KCTD20 MUTATION ANALYSIS"
[1] 3
  KCTD20 MUTATED KCTD20 WILD-TYPE 
               5              368 
  KCTD20 MUTATED KCTD20 WILD-TYPE 
               5              368 
[1] "GPR110 MUTATION ANALYSIS"
[1] 3
  GPR110 MUTATED GPR110 WILD-TYPE 
               6              367 
  GPR110 MUTATED GPR110 WILD-TYPE 
               6              367 
[1] "CEP164 MUTATION ANALYSIS"
[1] 3
  CEP164 MUTATED CEP164 WILD-TYPE 
               9              364 
  CEP164 MUTATED CEP164 WILD-TYPE 
               9              364 
[1] "TCEAL6 MUTATION ANALYSIS"
[1] 3
  TCEAL6 MUTATED TCEAL6 WILD-TYPE 
               4              369 
  TCEAL6 MUTATED TCEAL6 WILD-TYPE 
               4              369 
[1] "DNAJC28 MUTATION ANALYSIS"
[1] 3
  DNAJC28 MUTATED DNAJC28 WILD-TYPE 
                4               369 
  DNAJC28 MUTATED DNAJC28 WILD-TYPE 
                4               369 
[1] "FOXI1 MUTATION ANALYSIS"
[1] 3
  FOXI1 MUTATED FOXI1 WILD-TYPE 
              5             368 
  FOXI1 MUTATED FOXI1 WILD-TYPE 
              5             368 
[1] "KRTAP5-7 MUTATION ANALYSIS"
[1] 3
  KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE 
                 4                369 
  KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE 
                 4                369 
[1] "JAK1 MUTATION ANALYSIS"
[1] 3
  JAK1 MUTATED JAK1 WILD-TYPE 
            14            359 
  JAK1 MUTATED JAK1 WILD-TYPE 
            14            359 
[1] "DENND4B MUTATION ANALYSIS"
[1] 3
  DENND4B MUTATED DENND4B WILD-TYPE 
               12               361 
  DENND4B MUTATED DENND4B WILD-TYPE 
               12               361 
[1] "BRD7 MUTATION ANALYSIS"
[1] 3
  BRD7 MUTATED BRD7 WILD-TYPE 
            10            363 
  BRD7 MUTATED BRD7 WILD-TYPE 
            10            363 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
             8            365 
  IDH1 MUTATED IDH1 WILD-TYPE 
             8            365 
[1] "CNGA3 MUTATION ANALYSIS"
[1] 3
  CNGA3 MUTATED CNGA3 WILD-TYPE 
             11             362 
  CNGA3 MUTATED CNGA3 WILD-TYPE 
             11             362 
[1] "PLA2G3 MUTATION ANALYSIS"
[1] 3
  PLA2G3 MUTATED PLA2G3 WILD-TYPE 
               6              367 
  PLA2G3 MUTATED PLA2G3 WILD-TYPE 
               6              367 
[1] "HLA-DPB1 MUTATION ANALYSIS"
[1] 3
  HLA-DPB1 MUTATED HLA-DPB1 WILD-TYPE 
                 5                368 
  HLA-DPB1 MUTATED HLA-DPB1 WILD-TYPE 
                 5                368 
[1] "ALMS1 MUTATION ANALYSIS"
[1] 3
  ALMS1 MUTATED ALMS1 WILD-TYPE 
             24             349 
  ALMS1 MUTATED ALMS1 WILD-TYPE 
             24             349 
[1] "NUCB2 MUTATION ANALYSIS"
[1] 3
  NUCB2 MUTATED NUCB2 WILD-TYPE 
              3             370 
  NUCB2 MUTATED NUCB2 WILD-TYPE 
              3             370 
[1] "BAZ2A MUTATION ANALYSIS"
[1] 3
  BAZ2A MUTATED BAZ2A WILD-TYPE 
             11             362 
  BAZ2A MUTATED BAZ2A WILD-TYPE 
             11             362 
[1] "TAF1B MUTATION ANALYSIS"
[1] 3
  TAF1B MUTATED TAF1B WILD-TYPE 
              6             367 
  TAF1B MUTATED TAF1B WILD-TYPE 
              6             367 
[1] "C1ORF125 MUTATION ANALYSIS"
[1] 3
  C1ORF125 MUTATED C1ORF125 WILD-TYPE 
                11                362 
  C1ORF125 MUTATED C1ORF125 WILD-TYPE 
                11                362 
[1] "AR MUTATION ANALYSIS"
[1] 3
  AR MUTATED AR WILD-TYPE 
          10          363 
  AR MUTATED AR WILD-TYPE 
          10          363 
[1] "SPHK1 MUTATION ANALYSIS"
[1] 3
  SPHK1 MUTATED SPHK1 WILD-TYPE 
              6             367 
  SPHK1 MUTATED SPHK1 WILD-TYPE 
              6             367 
[1] "CREB3L3 MUTATION ANALYSIS"
[1] 3
  CREB3L3 MUTATED CREB3L3 WILD-TYPE 
                5               368 
  CREB3L3 MUTATED CREB3L3 WILD-TYPE 
                5               368 
[1] "LFNG MUTATION ANALYSIS"
[1] 3
  LFNG MUTATED LFNG WILD-TYPE 
             7            366 
  LFNG MUTATED LFNG WILD-TYPE 
             7            366 
[1] "FZR1 MUTATION ANALYSIS"
[1] 3
  FZR1 MUTATED FZR1 WILD-TYPE 
             6            367 
  FZR1 MUTATED FZR1 WILD-TYPE 
             6            367 
[1] "TRIOBP MUTATION ANALYSIS"
[1] 3
  TRIOBP MUTATED TRIOBP WILD-TYPE 
              11              362 
  TRIOBP MUTATED TRIOBP WILD-TYPE 
              11              362 
[1] "GJB1 MUTATION ANALYSIS"
[1] 3
  GJB1 MUTATED GJB1 WILD-TYPE 
             3            370 
  GJB1 MUTATED GJB1 WILD-TYPE 
             3            370 
[1] "DYRK1A MUTATION ANALYSIS"
[1] 3
  DYRK1A MUTATED DYRK1A WILD-TYPE 
               7              366 
  DYRK1A MUTATED DYRK1A WILD-TYPE 
               7              366 
[1] "TNPO1 MUTATION ANALYSIS"
[1] 3
  TNPO1 MUTATED TNPO1 WILD-TYPE 
              9             364 
  TNPO1 MUTATED TNPO1 WILD-TYPE 
              9             364 
[1] "PDZD4 MUTATION ANALYSIS"
[1] 3
  PDZD4 MUTATED PDZD4 WILD-TYPE 
              4             369 
  PDZD4 MUTATED PDZD4 WILD-TYPE 
              4             369 
[1] "CCNA2 MUTATION ANALYSIS"
[1] 3
  CCNA2 MUTATED CCNA2 WILD-TYPE 
              5             368 
  CCNA2 MUTATED CCNA2 WILD-TYPE 
              5             368 
[1] "AHCTF1 MUTATION ANALYSIS"
[1] 3
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
               8              365 
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
               8              365 
[1] "RXRB MUTATION ANALYSIS"
[1] 3
  RXRB MUTATED RXRB WILD-TYPE 
             8            365 
  RXRB MUTATED RXRB WILD-TYPE 
             8            365 
[1] "PARP1 MUTATION ANALYSIS"
[1] 3
  PARP1 MUTATED PARP1 WILD-TYPE 
              5             368 
  PARP1 MUTATED PARP1 WILD-TYPE 
              5             368 
[1] "NBEA MUTATION ANALYSIS"
[1] 3
  NBEA MUTATED NBEA WILD-TYPE 
            21            352 
  NBEA MUTATED NBEA WILD-TYPE 
            21            352 
[1] "H6PD MUTATION ANALYSIS"
[1] 3
  H6PD MUTATED H6PD WILD-TYPE 
             5            368 
  H6PD MUTATED H6PD WILD-TYPE 
             5            368 
[1] "VPS4B MUTATION ANALYSIS"
[1] 3
  VPS4B MUTATED VPS4B WILD-TYPE 
              5             368 
  VPS4B MUTATED VPS4B WILD-TYPE 
              5             368 
[1] "HNRNPL MUTATION ANALYSIS"
[1] 3
  HNRNPL MUTATED HNRNPL WILD-TYPE 
               8              365 
  HNRNPL MUTATED HNRNPL WILD-TYPE 
               8              365 
[1] "FILIP1 MUTATION ANALYSIS"
[1] 3
  FILIP1 MUTATED FILIP1 WILD-TYPE 
              13              360 
  FILIP1 MUTATED FILIP1 WILD-TYPE 
              13              360 
[1] "FAM22F MUTATION ANALYSIS"
[1] 3
  FAM22F MUTATED FAM22F WILD-TYPE 
               4              369 
  FAM22F MUTATED FAM22F WILD-TYPE 
               4              369 
[1] "GPSM2 MUTATION ANALYSIS"
[1] 3
  GPSM2 MUTATED GPSM2 WILD-TYPE 
              4             369 
  GPSM2 MUTATED GPSM2 WILD-TYPE 
              4             369 
[1] "RCCD1 MUTATION ANALYSIS"
[1] 3
  RCCD1 MUTATED RCCD1 WILD-TYPE 
              5             368 
  RCCD1 MUTATED RCCD1 WILD-TYPE 
              5             368 
[1] "PTGR1 MUTATION ANALYSIS"
[1] 3
  PTGR1 MUTATED PTGR1 WILD-TYPE 
              5             368 
  PTGR1 MUTATED PTGR1 WILD-TYPE 
              5             368 
[1] "SAMM50 MUTATION ANALYSIS"
[1] 3
  SAMM50 MUTATED SAMM50 WILD-TYPE 
               3              370 
  SAMM50 MUTATED SAMM50 WILD-TYPE 
               3              370 
[1] "PBRM1 MUTATION ANALYSIS"
[1] 3
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              9             364 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              9             364 
[1] "SGK269 MUTATION ANALYSIS"
[1] 3
  SGK269 MUTATED SGK269 WILD-TYPE 
               8              365 
  SGK269 MUTATED SGK269 WILD-TYPE 
               8              365 
[1] "LEO1 MUTATION ANALYSIS"
[1] 3
  LEO1 MUTATED LEO1 WILD-TYPE 
             5            368 
  LEO1 MUTATED LEO1 WILD-TYPE 
             5            368 
[1] "CD97 MUTATION ANALYSIS"
[1] 3
  CD97 MUTATED CD97 WILD-TYPE 
             5            368 
  CD97 MUTATED CD97 WILD-TYPE 
             5            368 
[1] "SKA3 MUTATION ANALYSIS"
[1] 3
  SKA3 MUTATED SKA3 WILD-TYPE 
             4            369 
  SKA3 MUTATED SKA3 WILD-TYPE 
             4            369 
[1] "CBX4 MUTATION ANALYSIS"
[1] 3
  CBX4 MUTATED CBX4 WILD-TYPE 
             6            367 
  CBX4 MUTATED CBX4 WILD-TYPE 
             6            367 
[1] "MTA1 MUTATION ANALYSIS"
[1] 3
  MTA1 MUTATED MTA1 WILD-TYPE 
             6            367 
  MTA1 MUTATED MTA1 WILD-TYPE 
             6            367 
[1] "CRIP3 MUTATION ANALYSIS"
[1] 3
  CRIP3 MUTATED CRIP3 WILD-TYPE 
              6             367 
  CRIP3 MUTATED CRIP3 WILD-TYPE 
              6             367 
[1] "NR4A2 MUTATION ANALYSIS"
[1] 3
  NR4A2 MUTATED NR4A2 WILD-TYPE 
              6             367 
  NR4A2 MUTATED NR4A2 WILD-TYPE 
              6             367 
[1] "HNF1A MUTATION ANALYSIS"
[1] 3
  HNF1A MUTATED HNF1A WILD-TYPE 
              8             365 
  HNF1A MUTATED HNF1A WILD-TYPE 
              8             365 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
             6            367 
  KRAS MUTATED KRAS WILD-TYPE 
             6            367 
[1] "PGBD1 MUTATION ANALYSIS"
[1] 3
  PGBD1 MUTATED PGBD1 WILD-TYPE 
              3             370 
  PGBD1 MUTATED PGBD1 WILD-TYPE 
              3             370 
[1] "LATS1 MUTATION ANALYSIS"
[1] 3
  LATS1 MUTATED LATS1 WILD-TYPE 
              7             366 
  LATS1 MUTATED LATS1 WILD-TYPE 
              7             366 
[1] "KEAP1 MUTATION ANALYSIS"
[1] 3
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             17             356 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             17             356 
[1] "SENP6 MUTATION ANALYSIS"
[1] 3
  SENP6 MUTATED SENP6 WILD-TYPE 
             11             362 
  SENP6 MUTATED SENP6 WILD-TYPE 
             11             362 
[1] "FKBP4 MUTATION ANALYSIS"
[1] 3
  FKBP4 MUTATED FKBP4 WILD-TYPE 
              4             369 
  FKBP4 MUTATED FKBP4 WILD-TYPE 
              4             369 
[1] "FOXK2 MUTATION ANALYSIS"
[1] 3
  FOXK2 MUTATED FOXK2 WILD-TYPE 
              6             367 
  FOXK2 MUTATED FOXK2 WILD-TYPE 
              6             367 
[1] "DSPP MUTATION ANALYSIS"
[1] 3
  DSPP MUTATED DSPP WILD-TYPE 
            21            352 
  DSPP MUTATED DSPP WILD-TYPE 
            21            352 
[1] "C10ORF28 MUTATION ANALYSIS"
[1] 3
  C10ORF28 MUTATED C10ORF28 WILD-TYPE 
                 4                369 
  C10ORF28 MUTATED C10ORF28 WILD-TYPE 
                 4                369 
[1] "PRAMEF4 MUTATION ANALYSIS"
[1] 3
  PRAMEF4 MUTATED PRAMEF4 WILD-TYPE 
                4               369 
  PRAMEF4 MUTATED PRAMEF4 WILD-TYPE 
                4               369 
[1] "RPS6KA5 MUTATION ANALYSIS"
[1] 3
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
                5               368 
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
                5               368 
[1] "DDX42 MUTATION ANALYSIS"
[1] 3
  DDX42 MUTATED DDX42 WILD-TYPE 
              6             367 
  DDX42 MUTATED DDX42 WILD-TYPE 
              6             367 
[1] "RHCG MUTATION ANALYSIS"
[1] 3
  RHCG MUTATED RHCG WILD-TYPE 
             4            369 
  RHCG MUTATED RHCG WILD-TYPE 
             4            369 
[1] "SWAP70 MUTATION ANALYSIS"
[1] 3
  SWAP70 MUTATED SWAP70 WILD-TYPE 
               5              368 
  SWAP70 MUTATED SWAP70 WILD-TYPE 
               5              368 
[1] "BIN1 MUTATION ANALYSIS"
[1] 3
  BIN1 MUTATED BIN1 WILD-TYPE 
             4            369 
  BIN1 MUTATED BIN1 WILD-TYPE 
             4            369 
[1] "SMARCA4 MUTATION ANALYSIS"
[1] 3
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               11               362 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               11               362 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "HISTOLOGICAL_TYPE"                   
[15] "RESIDUAL_TUMOR"                      
[16] "RACE"                                
[17] "ETHNICITY"                           

Input Data has 17 rows and 373 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=64,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=122,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=221,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_LAST_KNOWN_ALIVE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 373 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"    "PATHOLOGIC_STAGE"  "PATHOLOGY_T_STAGE"
 [4] "PATHOLOGY_N_STAGE" "PATHOLOGY_M_STAGE" "GENDER"           
 [7] "RADIATION_THERAPY" "HISTOLOGICAL_TYPE" "RESIDUAL_TUMOR"   
[10] "RACE"              "ETHNICITY"        
YEARS_TO_BIRTH, nv=64, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=9, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
184  94  79  13 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
184  94  79  13 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
184  94  79  13 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
184  94  79  13 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2              0   1
  TP53 MUTATED    70  43
  TP53 WILD-TYPE 167  87
  TP53 MUTATED TP53 WILD-TYPE 
           113            254 
  TP53 MUTATED TP53 WILD-TYPE 
            43             87 
$`TP53 MUTATED`
TCGA-4R-AA8I TCGA-BC-A5W4 TCGA-DD-AADV TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-FV-A3I1 
        8.61        17.98        18.87        21.83        18.90         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A7M9 TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-XR-A8TG 
        6.38        81.73         1.84         0.76         7.04        29.52 
TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9H4 TCGA-2Y-A9HA TCGA-5C-AAPD TCGA-BC-A10R 
       23.80        24.89        47.74         1.18         0.66        10.13 
TCGA-BC-A10U TCGA-BC-A216 TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A3EP 
       27.52        44.42        22.36        14.60        18.48        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.66         4.24         8.22         4.24         3.32         9.86 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IG TCGA-CC-A7II 
        9.96        10.36         9.99         8.94         9.83        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-DD-A114 
       12.56         8.61         4.60        11.31         9.17        37.78 
TCGA-DD-A11A TCGA-DD-A1EB TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EL 
        2.60        66.31        11.47        45.11         6.02        13.64 
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A7 TCGA-DD-AACB TCGA-DD-AACE TCGA-DD-AACF 
        5.62        25.81        13.78        76.41        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
       15.42         3.52        58.16        14.20        59.31        51.52 
TCGA-DD-AACV TCGA-DD-AACZ TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADB 
       50.33         5.62        42.58        44.22        40.08        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADW TCGA-DD-AAE0 
       13.97        40.47        20.91        29.52        19.30        18.25 
TCGA-DD-AAE6 TCGA-DD-AAED TCGA-DD-AAEI TCGA-DD-AAVU TCGA-DD-AAVV TCGA-ED-A459 
        4.64        25.08        50.33        72.39        80.71        29.92 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ES-A2HT TCGA-FV-A496 TCGA-FV-A4ZQ 
        0.20        14.04        13.15        14.40         0.33         0.39 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Z TCGA-G3-A3CJ TCGA-G3-A5SJ TCGA-G3-A5SM 
       53.79        28.27        21.53        19.53        22.95        17.10 
TCGA-G3-A7M6 TCGA-G3-AAV4 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-K7-A5RG TCGA-K7-AAU7 
       20.78         0.89        11.87        28.90        17.06        11.80 
TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A8LF TCGA-QA-A7B7 TCGA-RC-A6M6 TCGA-RC-A7SB 
       22.95        20.71        26.27         3.09         0.30        19.33 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.39        15.52        36.10        19.76        16.44         1.71 
TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-YA-A8S7 TCGA-ZP-A9D2 
       11.34        12.99        20.22        13.55        25.15 

$`TP53 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A110 TCGA-BC-A112 TCGA-BD-A3ER 
       83.24        11.74        38.40        69.57         5.03        36.66 
TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AAE7 TCGA-DD-AAEG TCGA-EP-A3JL 
        0.36        90.28        26.83        21.17        23.64         9.96 
TCGA-ES-A2HS TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF TCGA-KR-A7K0 
       22.62        30.74        22.13        22.06        20.75         2.14 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-UB-AA0V TCGA-XR-A8TC TCGA-ZP-A9D1 
       31.27        12.72        24.56        10.32        44.02         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ 
       40.80        53.39        63.75        41.79        80.28        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H8 
      120.82        40.41        56.91        49.84        18.25        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1C 
       22.92         8.55        13.02        10.78        10.59        17.10 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A10W 
       14.76         1.51        27.91        37.32        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A217 TCGA-BC-A3KF TCGA-BD-A2L6 
       25.32        23.38         1.12        45.93         0.26        44.81 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A3MC 
        2.86         3.19         3.39         3.35         7.20        11.93 
TCGA-CC-A5UC TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IH TCGA-CC-A7IL TCGA-CC-A8HS 
       11.41         7.13        21.34        12.00         9.14         9.86 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        6.94         8.15        79.73        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EK 
       19.79        75.65        12.95        49.15        33.04        18.35 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14        27.19        55.69        19.76         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NA 
       17.59        20.12       102.74       107.11        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ 
       32.52        21.70        30.97        26.37        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACH TCGA-DD-AACI 
       11.41        75.65        55.40        12.53         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACT 
       69.11         0.30        42.81        61.68        13.64        51.35 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
       46.82         5.59        47.67         4.50        18.54        21.63 
TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       22.09        40.54        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       35.05        34.49         0.39        14.89        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE1 TCGA-DD-AAE2 
       66.67        15.58        18.21        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEH 
       18.61        19.99        23.74        15.72        26.63        25.78 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVW 
       35.08        90.48        89.69        82.62        59.93        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        60.99 
TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       53.69        26.93        28.08        13.91        13.35         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
        0.20        12.82        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        20.61        19.59         0.62        11.93 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10        27.88        12.03         0.03 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
       13.68        51.06        14.86        25.64         5.92        19.23 
TCGA-G3-A5SI TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A7M5 TCGA-G3-A7M7 TCGA-G3-A7M8 
       25.25        24.46        20.42        14.70        11.87        14.14 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 
       15.78        15.65        11.80        12.23        13.55        11.64 
TCGA-G3-AAV6 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A6G5 
        2.14         1.02         2.20         2.99        37.71        16.83 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       27.25        29.79        13.97        12.03         9.57        16.67 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A6M4 
        7.53        10.85        58.88        17.69        21.01         0.72 
TCGA-RC-A6M5 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-UB-A7MA TCGA-UB-A7ME TCGA-UB-AA0U 
        0.49        21.04        19.04        27.88        15.98        10.75 
TCGA-WQ-A9G7 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
        0.99        24.85        18.28        33.86        30.41        22.78 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       35.77        25.71        23.21        35.87        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  TP53 MUTATED TP53 WILD-TYPE 
          0.20           0.03 
  TP53 MUTATED TP53 WILD-TYPE 
         81.73         120.82 
  TP53 MUTATED TP53 WILD-TYPE 
        15.420         21.255 
[1] "0.2 - 81.7 (15.4)"  "0.0 - 120.8 (21.3)"
[1] "hr=" "1.5"
D1V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TP53 MUTATED        50       33         0         20          3          2
  TP53 WILD-TYPE     124       53         3         44          6          7
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  TP53 MUTATED          0         0         0
  TP53 WILD-TYPE        2         1         2
D1V3, multiclass
            clus
vv           TP53 MUTATED TP53 WILD-TYPE
  STAGE I              50            124
  STAGE II             33             53
  STAGE III             0              3
  STAGE IIIA           20             44
  STAGE IIIB            3              6
  STAGE IIIC            2              7
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TP53 MUTATED    51  37  23   3
  TP53 WILD-TYPE 133  57  56  10
D1V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1           51            133
  T2           37             57
  T3           23             56
  T4            3             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
                cls
clus               0   1
  TP53 MUTATED    74   0
  TP53 WILD-TYPE 180   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     74    0
  TP53 WILD-TYPE  180    4
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           74            180
  1            0              4
[1] 2 2
[1] FALSE
D1V6, binary
                cls
clus               0   1
  TP53 MUTATED    85   0
  TP53 WILD-TYPE 184   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     85    0
  TP53 WILD-TYPE  184    4
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           85            184
  1            0              4
[1] 2 2
[1] FALSE
D1V7, binary
                cls
clus               0   1
  TP53 MUTATED    24  90
  TP53 WILD-TYPE  97 162
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     24   90
  TP53 WILD-TYPE   97  162
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           24             97
  MALE             90            162
[1] 2 2
[1] FALSE
D1V8, binary
                cls
clus               0   1
  TP53 MUTATED   103   3
  TP53 WILD-TYPE 238   6
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    103    3
  TP53 WILD-TYPE  238    6
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO           103            238
  YES            3              6
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  TP53 MUTATED                         0                      112
  TP53 WILD-TYPE                       3                      251
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  TP53 MUTATED                                  2
  TP53 WILD-TYPE                                5
D1V9, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              3
  HEPATOCELLULAR CARCINOMA                  112            251
  HEPATOCHOLANGIOCARCINOMA (MIXED)            2              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TP53 MUTATED   100   4   0   9
  TP53 WILD-TYPE 227  12   1  13
D1V10, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0          100            227
  R1            4             12
  R2            0              1
  RX            9             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TP53 MUTATED                                  1    58
  TP53 WILD-TYPE                                1   102
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED                          12    41
  TP53 WILD-TYPE                         5   143
D1V11, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              1
  ASIAN                                      58            102
  BLACK OR AFRICAN AMERICAN                  12              5
  WHITE                                      41            143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, binary
                cls
clus               0   1
  TP53 MUTATED     4 107
  TP53 WILD-TYPE  14 230
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      4  107
  TP53 WILD-TYPE   14  230
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                4             14
  NOT HISPANIC OR LATINO          107            230
[1] 2 2
[1] FALSE

Clustering(2) Variable = CTNNB1 MUTATION ANALYSIS
D2V1, survival
                  sevent
clus2                0   1
  CTNNB1 MUTATED    65  31
  CTNNB1 WILD-TYPE 172  99
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              96              271 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              31               99 
$`CTNNB1 MUTATED`
TCGA-4R-AA8I TCGA-DD-A4NI TCGA-EP-A3JL TCGA-G3-A6UC TCGA-KR-A7K0 TCGA-MI-A75H 
        8.61        26.83         9.96        22.06         2.14        24.56 
TCGA-2Y-A9H1 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5R-AA1C 
       40.41         1.18         8.55        13.02        10.78        17.10 
TCGA-BC-A10U TCGA-CC-5262 TCGA-CC-A5UD TCGA-CC-A7IH TCGA-CC-A7IK TCGA-CC-A7IL 
       27.52         3.39         9.99        12.00         8.61         9.14 
TCGA-CC-A9FW TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1ED 
        8.15        53.33         7.33        51.29        79.40        75.65 
TCGA-DD-A1EE TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y 
       11.47        33.04        13.64        21.14        27.19         5.62 
TCGA-DD-A3A4 TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A73A TCGA-DD-A73D 
       20.12        30.97        39.78        56.25        23.93        22.78 
TCGA-DD-A73E TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACJ 
        1.45         0.53        75.65        76.41        12.53        69.11 
TCGA-DD-AACK TCGA-DD-AACP TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AADD TCGA-DD-AADE 
        0.30        13.64         5.59         4.50        40.47        39.52 
TCGA-DD-AADG TCGA-DD-AADM TCGA-DD-AADU TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAEE 
       37.64         0.39        18.21        18.61        23.74        26.63 
TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVX TCGA-DD-AAVY 
       25.78        35.08        90.48        89.69        56.48        64.77 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A12J 
       65.39        60.99        53.69         0.20        13.15        18.74 
TCGA-EP-A26S TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A2QQ TCGA-FV-A4ZQ TCGA-G3-A25Z 
       19.99         0.62        11.93        23.97         0.39        21.53 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL TCGA-G3-AAV1 TCGA-G3-AAV2 
       19.53        19.23        22.95        20.42        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-K7-A6G5 TCGA-LG-A9QD 
       13.55         0.89        11.64         2.14        16.83        12.03 
TCGA-MI-A75C TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A6M4 TCGA-RG-A7D4 TCGA-UB-A7MC 
        9.57        26.27        17.69         0.72        36.10        16.44 
TCGA-UB-A7MD TCGA-WX-AA47 TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9D4 TCGA-ZS-A9CG 
        1.71        18.28        22.78        35.77        12.99        11.21 

$`CTNNB1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        11.74        38.40        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 
       36.66         0.36        90.28        18.87        21.17        21.83 
TCGA-DD-AAEA TCGA-DD-AAEG TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP 
       18.90        23.64        22.62         8.12         6.38        81.73 
TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K7 TCGA-LG-A6GG 
       30.74        22.13         1.84        20.75        31.27        12.72 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       24.89        27.88       120.82        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1D 
       18.25        20.81        22.92        10.59         0.66        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10W 
        1.51        27.91        37.32        10.13        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        14.60        18.48        44.81        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-5264 
        4.24         8.22         2.86         3.19         4.24         3.35 
TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        7.20         3.32         9.86         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7II 
       11.41         8.94         7.13        21.34         9.83        13.12 
TCGA-CC-A7IJ TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
       12.56         9.86         4.60        11.31         9.17         6.94 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B 
       79.73        37.78        83.57       113.00         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EG 
       21.76        90.71        66.31        19.79        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 
       49.15         6.02        18.35        55.69        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
        7.66        70.06        17.59       102.74       107.11        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NG TCGA-DD-A4NH 
       30.61        33.14        32.52        21.70        26.37        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       30.51        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-A73G 
       80.75        78.84         9.30        23.05        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       13.48        11.41        55.40        71.80        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
        6.41        53.19         3.52        58.16        42.81        61.68 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       14.20        59.31        51.35        51.52        50.33        46.82 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
       47.67         5.62        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADF 
       22.09        40.08        40.54        40.83        13.97         3.78 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO 
       35.67        35.05        34.49        20.91        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADW TCGA-DD-AADY 
       15.06        14.33        66.67        15.58        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAEB 
       18.25        18.15        20.98        19.99         4.64        15.72 
TCGA-DD-AAED TCGA-DD-AAEI TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       25.08        50.33        82.62        59.93        72.39        80.71 
TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       76.18        62.47        66.25        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO 
       13.91        13.35         9.73         0.20        12.82        14.04 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A2KA TCGA-EP-A2KB 
       13.41        13.35         1.84         0.20        20.61        19.59 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       14.40        60.89        19.10        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.33        13.68        51.06        53.79        28.27        14.86 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SI TCGA-G3-A5SK TCGA-G3-A5SM TCGA-G3-A7M5 
       25.64         5.92        25.25        24.46        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV7 
       20.78        11.87        14.14        15.78        15.65        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-MI-A75E TCGA-MI-A75G 
       11.80        27.25        29.79        13.97        16.67        22.95 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 
       20.71         7.53        10.85        58.88        21.01         3.09 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L 
       15.52        27.88        19.76        15.98        10.75        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-XR-A8TD TCGA-XR-A8TE 
        0.99        12.99        20.22        24.85        33.86        30.41 
TCGA-YA-A8S7 TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZS-A9CD 
       13.55        25.71        23.21        35.87        25.15        45.57 
TCGA-ZS-A9CF 
       79.30 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
            0.20             0.03 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           90.48           120.82 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          18.445           20.610 
[1] "0.2 - 90.5 (18.4)"  "0.0 - 120.8 (20.6)"
[1] "hr=" "1"  
D2V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CTNNB1 MUTATED        45       23         1         18          2          3
  CTNNB1 WILD-TYPE     129       63         2         46          7          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  CTNNB1 MUTATED          1         0         0
  CTNNB1 WILD-TYPE        1         1         2
D2V3, multiclass
            clus
vv           CTNNB1 MUTATED CTNNB1 WILD-TYPE
  STAGE I                45              129
  STAGE II               23               63
  STAGE III               1                2
  STAGE IIIA             18               46
  STAGE IIIB              2                7
  STAGE IIIC              3                6
  STAGE IV                1                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CTNNB1 MUTATED    48  24  22   2
  CTNNB1 WILD-TYPE 136  70  57  11
D2V4, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  T1             48              136
  T2             24               70
  T3             22               57
  T4              2               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    68   1
  CTNNB1 WILD-TYPE 186   3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     68    1
  CTNNB1 WILD-TYPE  186    3
   clus
vv  CTNNB1 MUTATED CTNNB1 WILD-TYPE
  0             68              186
  1              1                3
[1] 2 2
[1] FALSE
D2V6, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    70   1
  CTNNB1 WILD-TYPE 199   3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     70    1
  CTNNB1 WILD-TYPE  199    3
   clus
vv  CTNNB1 MUTATED CTNNB1 WILD-TYPE
  0             70              199
  1              1                3
[1] 2 2
[1] FALSE
D2V7, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    14  83
  CTNNB1 WILD-TYPE 107 169
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     14   83
  CTNNB1 WILD-TYPE  107  169
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  FEMALE             14              107
  MALE               83              169
[1] 2 2
[1] FALSE
D2V8, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    87   5
  CTNNB1 WILD-TYPE 254   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     87    5
  CTNNB1 WILD-TYPE  254    4
     clus
vv    CTNNB1 MUTATED CTNNB1 WILD-TYPE
  NO              87              254
  YES              5                4
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  CTNNB1 MUTATED                         0                       97
  CTNNB1 WILD-TYPE                       3                      266
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  CTNNB1 MUTATED                                  0
  CTNNB1 WILD-TYPE                                7
D2V9, multiclass
                                  clus
vv                                 CTNNB1 MUTATED CTNNB1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                3
  HEPATOCELLULAR CARCINOMA                     97              266
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CTNNB1 MUTATED    86   3   1   3
  CTNNB1 WILD-TYPE 241  13   0  19
D2V10, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  R0             86              241
  R1              3               13
  R2              1                0
  RX              3               19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTNNB1 MUTATED                                  1    41
  CTNNB1 WILD-TYPE                                1   119
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CTNNB1 MUTATED                           6    47
  CTNNB1 WILD-TYPE                        11   137
D2V11, multiclass
                                  clus
vv                                 CTNNB1 MUTATED CTNNB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                1
  ASIAN                                        41              119
  BLACK OR AFRICAN AMERICAN                     6               11
  WHITE                                        47              137
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED     4  92
  CTNNB1 WILD-TYPE  14 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      4   92
  CTNNB1 WILD-TYPE   14  245
                        clus
vv                       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  HISPANIC OR LATINO                  4               14
  NOT HISPANIC OR LATINO             92              245
[1] 2 2
[1] FALSE

Clustering(3) Variable = AXIN1 MUTATION ANALYSIS
D3V1, survival
                 sevent
clus2               0   1
  AXIN1 MUTATED    15   7
  AXIN1 WILD-TYPE 222 123
  AXIN1 MUTATED AXIN1 WILD-TYPE 
             22             345 
  AXIN1 MUTATED AXIN1 WILD-TYPE 
              7             123 
$`AXIN1 MUTATED`
TCGA-2Y-A9H7 TCGA-DD-AAEA TCGA-ES-A2HS TCGA-FV-A3R2 TCGA-XR-A8TC TCGA-CC-A5UC 
       38.40        18.90        22.62         6.38        44.02        11.41 
TCGA-CC-A5UE TCGA-CC-A9FS TCGA-DD-A11B TCGA-DD-A1EH TCGA-DD-A39Z TCGA-DD-AADO 
        8.94         6.94         0.46        49.15        19.76        14.89 
TCGA-DD-AADS TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVZ 
       15.58        18.15         4.64        59.93        72.39        62.47 
TCGA-ED-A8O5 TCGA-G3-A3CJ TCGA-G3-AAV7 TCGA-XR-A8TF 
       13.35        19.53        11.87        22.78 

$`AXIN1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        11.74         8.61        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-G3-A25W 
       21.83        23.64         9.96         8.12        81.73        30.74 
TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 
       22.13        22.06         1.84        20.75         2.14        31.27 
TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG 
       12.72        24.56         0.76         7.04        10.32        29.52 
TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW 
        0.69        40.80        23.80        53.39        63.75        41.79 
TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 
       80.28        24.89        27.88       120.82        40.41        56.91 
TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       49.84        47.74        18.25        20.81        22.92         1.18 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C 
        8.55        13.02        10.78        10.59         0.66        17.10 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T 
       14.76         1.51        27.91        37.32        10.13        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 
       27.52         2.99        25.32        23.38         1.12        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 
       45.93         0.26        22.36        14.60        18.48        44.81 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 
       13.45         0.66         4.24         8.22         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 
        3.39         4.24         3.35         7.20         3.32         9.86 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IF 
        9.96        10.36        11.93         9.99         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        9.83        12.00        13.12        12.56         8.61         9.14 
TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A113 
        9.86         4.60        11.31         9.17         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        11.47        12.95        45.11         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       18.35        13.64        21.14        27.19        55.69         5.62 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE 
      107.11        13.78        30.61        33.14        32.52        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        26.37        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       35.67       114.35        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       76.41        55.40        12.53        71.80        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       42.81        61.68        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADU 
        0.39        29.52        15.06        14.33        66.67        18.21 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       19.30        18.25        18.25        20.98        18.61        19.99 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVV TCGA-DD-AAVW 
       35.08        90.48        89.69        82.62        80.71        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       56.48        64.77        66.25        65.39        60.99        53.69 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       29.92        26.93        28.08        13.91        13.35         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20        12.82         0.20        14.04        13.15        13.41 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        1.84         0.20        18.74        19.99        20.61        19.59 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        0.62        11.93        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S 
       27.88        12.03         0.03         0.33         0.39        13.68 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       51.06        53.79        28.27        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
        5.92        19.23        25.25        22.95        24.46        20.42 
TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       17.10        14.70        20.78        11.87        14.14        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.65        11.80        12.23        13.55         0.89        11.64 
TCGA-G3-AAV6 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        2.14        28.90         1.02         2.20         2.99        37.71 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06        16.83        11.80        27.25        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        26.27        17.69        21.01         3.09 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        15.52        36.10        27.88        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        1.71        15.98        10.75        11.34         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-YA-A8S7 
       20.22        24.85        18.28        33.86        30.41        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        25.71        23.21        35.87        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  AXIN1 MUTATED AXIN1 WILD-TYPE 
           0.46            0.03 
  AXIN1 MUTATED AXIN1 WILD-TYPE 
          72.39          120.82 
  AXIN1 MUTATED AXIN1 WILD-TYPE 
         18.525          19.990 
[1] "0.5 - 72.4 (18.5)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "1"  
D3V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AXIN1 MUTATED        13        5         1          3          1          0
  AXIN1 WILD-TYPE     161       81         2         61          8          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  AXIN1 MUTATED          1         0         0
  AXIN1 WILD-TYPE        1         1         2
D3V3, multiclass
            clus
vv           AXIN1 MUTATED AXIN1 WILD-TYPE
  STAGE I               13             161
  STAGE II               5              81
  STAGE III              1               2
  STAGE IIIA             3              61
  STAGE IIIB             1               8
  STAGE IIIC             0               9
  STAGE IV               1               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AXIN1 MUTATED    13   6   4   1
  AXIN1 WILD-TYPE 171  88  75  12
D3V4, multiclass
    clus
vv   AXIN1 MUTATED AXIN1 WILD-TYPE
  T1            13             171
  T2             6              88
  T3             4              75
  T4             1              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
                 cls
clus                0   1
  AXIN1 MUTATED    19   0
  AXIN1 WILD-TYPE 235   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN1 MUTATED     19    0
  AXIN1 WILD-TYPE  235    4
   clus
vv  AXIN1 MUTATED AXIN1 WILD-TYPE
  0            19             235
  1             0               4
[1] 2 2
[1] FALSE
D3V6, binary
                 cls
clus                0   1
  AXIN1 MUTATED    18   1
  AXIN1 WILD-TYPE 251   3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN1 MUTATED     18    1
  AXIN1 WILD-TYPE  251    3
   clus
vv  AXIN1 MUTATED AXIN1 WILD-TYPE
  0            18             251
  1             1               3
[1] 2 2
[1] FALSE
D3V7, binary
                 cls
clus                0   1
  AXIN1 MUTATED     7  17
  AXIN1 WILD-TYPE 114 235
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN1 MUTATED      7   17
  AXIN1 WILD-TYPE  114  235
        clus
vv       AXIN1 MUTATED AXIN1 WILD-TYPE
  FEMALE             7             114
  MALE              17             235
[1] 2 2
[1] FALSE
D3V8, binary
                 cls
clus                0   1
  AXIN1 MUTATED    21   0
  AXIN1 WILD-TYPE 320   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN1 MUTATED     21    0
  AXIN1 WILD-TYPE  320    9
     clus
vv    AXIN1 MUTATED AXIN1 WILD-TYPE
  NO             21             320
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AXIN1 MUTATED                         0                       24
  AXIN1 WILD-TYPE                       3                      339
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  AXIN1 MUTATED                                  0
  AXIN1 WILD-TYPE                                7
D3V9, multiclass
                                  clus
vv                                 AXIN1 MUTATED AXIN1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                    24             339
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AXIN1 MUTATED    22   0   0   2
  AXIN1 WILD-TYPE 305  16   1  20
D3V10, multiclass
    clus
vv   AXIN1 MUTATED AXIN1 WILD-TYPE
  R0            22             305
  R1             0              16
  R2             0               1
  RX             2              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AXIN1 MUTATED                                  1    14
  AXIN1 WILD-TYPE                                1   146
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AXIN1 MUTATED                           0     8
  AXIN1 WILD-TYPE                        17   176
D3V11, multiclass
                                  clus
vv                                 AXIN1 MUTATED AXIN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               1
  ASIAN                                       14             146
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        8             176
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, binary
                 cls
clus                0   1
  AXIN1 MUTATED     3  20
  AXIN1 WILD-TYPE  15 317
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN1 MUTATED      3   20
  AXIN1 WILD-TYPE   15  317
                        clus
vv                       AXIN1 MUTATED AXIN1 WILD-TYPE
  HISPANIC OR LATINO                 3              15
  NOT HISPANIC OR LATINO            20             317
[1] 2 2
[1] FALSE

Clustering(4) Variable = RB1 MUTATION ANALYSIS
D4V1, survival
               sevent
clus2             0   1
  RB1 MUTATED    10  11
  RB1 WILD-TYPE 227 119
  RB1 MUTATED RB1 WILD-TYPE 
           21           346 
  RB1 MUTATED RB1 WILD-TYPE 
           11           119 
$`RB1 MUTATED`
TCGA-5C-AAPD TCGA-CC-A3MA TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A8HU TCGA-DD-A113 
        0.66         9.96        21.34         9.83        11.31        79.73 
TCGA-DD-A114 TCGA-DD-A1EE TCGA-DD-A4NE TCGA-DD-A4NJ TCGA-DD-AADM TCGA-DD-AADW 
       37.78        11.47        21.70        30.51         0.39        19.30 
TCGA-ED-A66Y TCGA-ED-A7PZ TCGA-G3-A25U TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A5SI 
        9.73         0.20        53.79        14.86        25.64        25.25 
TCGA-RC-A7S9 TCGA-UB-A7MB TCGA-WX-AA44 
       21.04        19.76        20.22 

$`RB1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       13.02        10.78        10.59        17.10        14.76         1.51 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        14.60        18.48        44.81        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.24         8.22         2.86         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC 
        3.35         7.20         3.32         9.86        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IH TCGA-CC-A7II 
       11.41         9.99         8.94         7.13        12.00        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HV 
       12.56         8.61         9.14         9.86         4.60         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        6.94         8.15        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       66.31        19.79        75.65        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NK 
       33.14        32.52        30.97        26.37        30.15        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        40.08        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       20.91        29.52        14.89        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       15.58        18.21        18.25        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
       18.61        19.99         4.64        23.74        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       26.63        25.78        50.33        35.08        90.48        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       82.62        59.93        72.39        80.71        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       64.77        62.47        66.25        65.39        60.99        53.69 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX 
       29.92        26.93        28.08        13.91        13.35         0.20 
TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
       12.82        14.04        13.15        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        20.61        19.59         0.62 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
TCGA-G3-A25V TCGA-G3-A25Z TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ 
       28.27        21.53         5.92        19.53        19.23        22.95 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       24.46        20.42        17.10        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        0.89        11.64         2.14        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       27.25        29.79        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       22.95        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       17.69        21.01         3.09         0.72         0.49         0.30 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       19.33        19.04        15.39        15.52        36.10        27.88 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 
       16.44         1.71        15.98        10.75        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       12.99        24.85        18.28        33.86        30.41        22.78 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       13.55        35.77        25.71        23.21        35.87        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        79.30        11.21 

  RB1 MUTATED RB1 WILD-TYPE 
         0.20          0.03 
  RB1 MUTATED RB1 WILD-TYPE 
        79.73        120.82 
  RB1 MUTATED RB1 WILD-TYPE 
       19.760        19.775 
[1] "0.2 - 79.7 (19.8)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.9"
D4V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  RB1 MUTATED         5        9         0          7          0          0
  RB1 WILD-TYPE     169       77         3         57          9          9
               vv
clus            STAGE IV STAGE IVA STAGE IVB
  RB1 MUTATED          0         0         0
  RB1 WILD-TYPE        2         1         2
D4V3, multiclass
            clus
vv           RB1 MUTATED RB1 WILD-TYPE
  STAGE I              5           169
  STAGE II             9            77
  STAGE III            0             3
  STAGE IIIA           7            57
  STAGE IIIB           0             9
  STAGE IIIC           0             9
  STAGE IV             0             2
  STAGE IVA            0             1
  STAGE IVB            0             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  RB1 MUTATED     5   9   7   0
  RB1 WILD-TYPE 179  85  72  13
D4V4, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  T1           5           179
  T2           9            85
  T3           7            72
  T4           0            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
               cls
clus              0   1
  RB1 MUTATED    17   0
  RB1 WILD-TYPE 237   4
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     17    0
  RB1 WILD-TYPE  237    4
   clus
vv  RB1 MUTATED RB1 WILD-TYPE
  0          17           237
  1           0             4
[1] 2 2
[1] FALSE
D4V6, binary
               cls
clus              0   1
  RB1 MUTATED    19   0
  RB1 WILD-TYPE 250   4
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     19    0
  RB1 WILD-TYPE  250    4
   clus
vv  RB1 MUTATED RB1 WILD-TYPE
  0          19           250
  1           0             4
[1] 2 2
[1] FALSE
D4V7, binary
               cls
clus              0   1
  RB1 MUTATED     9  12
  RB1 WILD-TYPE 112 240
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      9   12
  RB1 WILD-TYPE  112  240
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE           9           112
  MALE            12           240
[1] 2 2
[1] FALSE
D4V8, binary
               cls
clus              0   1
  RB1 MUTATED    20   1
  RB1 WILD-TYPE 321   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     20    1
  RB1 WILD-TYPE  321    8
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO           20           321
  YES           1             8
[1] 2 2
[1] FALSE
               vv
clus            FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  RB1 MUTATED                         0                       20
  RB1 WILD-TYPE                       3                      343
               vv
clus            HEPATOCHOLANGIOCARCINOMA (MIXED)
  RB1 MUTATED                                  1
  RB1 WILD-TYPE                                6
D4V9, multiclass
                                  clus
vv                                 RB1 MUTATED RB1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                    0             3
  HEPATOCELLULAR CARCINOMA                  20           343
  HEPATOCHOLANGIOCARCINOMA (MIXED)           1             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  RB1 MUTATED    20   0   0   1
  RB1 WILD-TYPE 307  16   1  21
D4V10, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  R0          20           307
  R1           0            16
  R2           0             1
  RX           1            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RB1 MUTATED                                  0    14
  RB1 WILD-TYPE                                2   146
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED                           1     6
  RB1 WILD-TYPE                        16   178
D4V11, multiclass
                                  clus
vv                                 RB1 MUTATED RB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                     14           146
  BLACK OR AFRICAN AMERICAN                  1            16
  WHITE                                      6           178
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, binary
               cls
clus              0   1
  RB1 MUTATED     2  19
  RB1 WILD-TYPE  16 318
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      2   19
  RB1 WILD-TYPE   16  318
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               2            16
  NOT HISPANIC OR LATINO          19           318
[1] 2 2
[1] FALSE

Clustering(5) Variable = ARID1A MUTATION ANALYSIS
D5V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED    13  17
  ARID1A WILD-TYPE 224 113
  ARID1A MUTATED ARID1A WILD-TYPE 
              30              337 
  ARID1A MUTATED ARID1A WILD-TYPE 
              17              113 
$`ARID1A MUTATED`
TCGA-DD-AAE7 TCGA-DD-AAEG TCGA-G3-A3CG TCGA-LG-A6GG TCGA-BC-A10W TCGA-CC-5258 
       21.17        23.64        22.13        12.72         2.99         4.24 
TCGA-CC-5262 TCGA-CC-A123 TCGA-CC-A5UD TCGA-CC-A9FS TCGA-DD-A1EE TCGA-DD-A1EH 
        3.39         7.20         9.99         6.94        11.47        49.15 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A4NR TCGA-DD-AACG 
       21.14        27.19        55.69         5.62         0.30        15.42 
TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AAVX TCGA-EP-A2KB TCGA-ES-A2HT TCGA-FV-A23B 
       15.06        66.67        56.48        19.59        14.40        60.89 
TCGA-G3-A3CJ TCGA-KR-A7K8 TCGA-UB-A7MD TCGA-UB-A7ME TCGA-XR-A8TF TCGA-ZS-A9CD 
       19.53        29.79         1.71        15.98        22.78        45.57 

$`ARID1A WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 
       21.83        18.90         9.96        22.62         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 
       81.73        30.74        22.06         1.84        20.75         2.14 
TCGA-KR-A7K7 TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC 
       31.27        24.56         0.76         7.04        10.32        44.02 
TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU 
       29.52         0.69        40.80        23.80        53.39        63.75 
TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       41.79        80.28        24.89        27.88       120.82        40.41 
TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       56.91        49.84        47.74        18.25        20.81        22.92 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
        1.18         8.55        13.02        10.78        10.59         0.66 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       17.10        14.76         1.51        27.91        37.32        10.13 
TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 
       27.52        27.52        25.32        23.38         1.12        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 
       45.93         0.26        22.36        14.60        18.48        44.81 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 
       13.45         0.66         8.22         2.86         3.19         4.24 
TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        3.35         3.32         9.86         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
       11.41         8.94         7.13        21.34         9.83        12.00 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT 
       13.12        12.56         8.61         9.14         9.86         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
       11.31         9.17         8.15        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.33       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       12.95        45.11         6.02        33.04        18.35        13.64 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       21.70        30.97        26.37        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS 
       56.25        29.56        73.81       108.76        12.26        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       35.67       114.35        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH 
       76.41        55.40        12.53        71.80        12.00         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
       53.19        69.11         0.30         3.52        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
       61.68        13.64        14.20        59.31        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       50.33        46.82         5.59        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       40.54        40.83        13.97        40.47        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       37.64        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       29.52        14.89        14.33        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        23.74        15.72        25.08        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        90.48        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       72.39        80.71        76.18        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        60.99        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A2QQ 
       18.74        19.99        20.61         0.62        11.93        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
       19.10        27.88        12.03         0.03         0.33         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z 
       13.68        51.06        53.79        28.27        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
       25.64         5.92        19.23        25.25        22.95        24.46 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       20.42        17.10        14.70        20.78        11.87        14.14 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       15.78        15.65        11.80        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       11.64         2.14        11.87        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 
        2.99        37.71        17.06        16.83        11.80        27.25 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       13.97        12.03         9.57        16.67        22.95        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        7.53        10.85        58.88        26.27        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB 
        3.09         0.72         0.49         0.30        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.04        15.39        15.52        36.10        27.88        19.76 
TCGA-UB-A7MC TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       16.44        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-YA-A8S7 TCGA-ZP-A9CV 
       24.85        18.28        33.86        30.41        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CF 
       25.71        23.21        35.87        25.15        12.99        79.30 
TCGA-ZS-A9CG 
       11.21 

  ARID1A MUTATED ARID1A WILD-TYPE 
            0.30             0.03 
  ARID1A MUTATED ARID1A WILD-TYPE 
           66.67           120.82 
  ARID1A MUTATED ARID1A WILD-TYPE 
          17.755           19.990 
[1] "0.3 - 66.7 (17.8)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "2"  
D5V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ARID1A MUTATED        15       10         2          3          0          1
  ARID1A WILD-TYPE     159       76         1         61          9          8
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  ARID1A MUTATED          0         0         0
  ARID1A WILD-TYPE        2         1         2
D5V3, multiclass
            clus
vv           ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                15              159
  STAGE II               10               76
  STAGE III               2                1
  STAGE IIIA              3               61
  STAGE IIIB              0                9
  STAGE IIIC              1                8
  STAGE IV                0                2
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ARID1A MUTATED    15  10   5   2
  ARID1A WILD-TYPE 169  84  74  11
D5V4, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  T1             15              169
  T2             10               84
  T3              5               74
  T4              2               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
                  cls
clus                 0   1
  ARID1A MUTATED    20   0
  ARID1A WILD-TYPE 234   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     20    0
  ARID1A WILD-TYPE  234    4
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0             20              234
  1              0                4
[1] 2 2
[1] FALSE
D5V6, binary
                  cls
clus                 0   1
  ARID1A MUTATED    23   0
  ARID1A WILD-TYPE 246   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     23    0
  ARID1A WILD-TYPE  246    4
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0             23              246
  1              0                4
[1] 2 2
[1] FALSE
D5V7, binary
                  cls
clus                 0   1
  ARID1A MUTATED     8  24
  ARID1A WILD-TYPE 113 228
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      8   24
  ARID1A WILD-TYPE  113  228
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE              8              113
  MALE               24              228
[1] 2 2
[1] FALSE
D5V8, binary
                  cls
clus                 0   1
  ARID1A MUTATED    27   2
  ARID1A WILD-TYPE 314   7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     27    2
  ARID1A WILD-TYPE  314    7
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO              27              314
  YES              2                7
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  ARID1A MUTATED                         0                       32
  ARID1A WILD-TYPE                       3                      331
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  ARID1A MUTATED                                  0
  ARID1A WILD-TYPE                                7
D5V9, multiclass
                                  clus
vv                                 ARID1A MUTATED ARID1A WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                3
  HEPATOCELLULAR CARCINOMA                     32              331
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ARID1A MUTATED    26   2   0   3
  ARID1A WILD-TYPE 301  14   1  19
D5V10, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0             26              301
  R1              2               14
  R2              0                1
  RX              3               19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID1A MUTATED                                  1    15
  ARID1A WILD-TYPE                                1   145
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED                           2    13
  ARID1A WILD-TYPE                        15   171
D5V11, multiclass
                                  clus
vv                                 ARID1A MUTATED ARID1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                1
  ASIAN                                        15              145
  BLACK OR AFRICAN AMERICAN                     2               15
  WHITE                                        13              171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, binary
                  cls
clus                 0   1
  ARID1A MUTATED     1  30
  ARID1A WILD-TYPE  17 307
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      1   30
  ARID1A WILD-TYPE   17  307
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  1               17
  NOT HISPANIC OR LATINO             30              307
[1] 2 2
[1] FALSE

Clustering(6) Variable = BAP1 MUTATION ANALYSIS
D6V1, survival
                sevent
clus2              0   1
  BAP1 MUTATED    15   6
  BAP1 WILD-TYPE 222 124
  BAP1 MUTATED BAP1 WILD-TYPE 
            21            346 
  BAP1 MUTATED BAP1 WILD-TYPE 
             6            124 
$`BAP1 MUTATED`
TCGA-2Y-A9H6 TCGA-2Y-A9GU TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-BC-A10Q TCGA-BC-A10R 
       11.74        63.75        56.91        49.84        37.32        10.13 
TCGA-CC-5260 TCGA-DD-A118 TCGA-DD-A1EF TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A73G 
        2.86       113.00        12.95        30.61        33.14       114.35 
TCGA-DD-AA3A TCGA-DD-AADA TCGA-DD-AAVR TCGA-ED-A4XI TCGA-ED-A7PX TCGA-FV-A3I0 
       13.48        40.54        82.62        26.93         0.20        27.88 
TCGA-G3-A25T TCGA-WQ-A9G7 TCGA-ZS-A9CG 
       51.06         0.99        11.21 

$`BAP1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        38.40         8.61        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       23.80        53.39        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
      120.82        40.41        47.74        18.25        20.81        22.92 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
        1.18         8.55        13.02        10.78        10.59         0.66 
TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10T TCGA-BC-A10U 
       17.10        14.76         1.51        27.91        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.66         4.24         8.22         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.35         7.20         3.32         9.86         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
       11.93        11.41         9.99         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        9.83        12.00        13.12        12.56         8.61         9.14 
TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.86         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A 
       79.73        37.78        83.57        53.33         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        11.47        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NB TCGA-DD-A4NE 
       20.12       102.74       107.11        13.78        32.52        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        26.37        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       35.67         0.53        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        71.80        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       69.11         0.30         3.52        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV 
       13.64        14.20        59.31        51.35        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       46.82         5.59        47.67         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB 
       21.63        42.58        44.22        22.09        40.08        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.05        34.49        20.91         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        23.74        15.72        25.08        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU 
       50.33        35.08        90.48        89.69        59.93        72.39 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A627 
       65.39        60.99        53.69        29.92        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
       13.35         9.73        12.82         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
       23.97        19.10        12.03         0.03         0.33         0.39 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       13.68        53.79        28.27        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
        5.92        19.53        19.23        25.25        22.95        24.46 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       20.42        17.10        14.70        20.78        11.87        14.14 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       15.78        15.65        11.80        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       11.64         2.14        11.87        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 
        2.99        37.71        17.06        16.83        11.80        27.25 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       29.79        13.97        12.03         9.57        16.67        22.95 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         7.53        10.85        58.88        26.27        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 
       21.01         3.09         0.72         0.49         0.30        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       19.33        19.04        15.39        15.52        36.10        27.88 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L 
       19.76        16.44         1.71        15.98        10.75        11.34 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE 
       12.99        20.22        24.85        18.28        33.86        30.41 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       22.78        13.55        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       25.15        12.99        45.57        79.30 

  BAP1 MUTATED BAP1 WILD-TYPE 
          0.20           0.03 
  BAP1 MUTATED BAP1 WILD-TYPE 
        114.35         120.82 
  BAP1 MUTATED BAP1 WILD-TYPE 
         30.61          19.56 
[1] "0.2 - 114.3 (30.6)" "0.0 - 120.8 (19.6)"
[1] "hr=" "1.8"
D6V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  BAP1 MUTATED         8        6         0          1          0          2
  BAP1 WILD-TYPE     166       80         3         63          9          7
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  BAP1 MUTATED          0         0         1
  BAP1 WILD-TYPE        2         1         1
D6V3, multiclass
            clus
vv           BAP1 MUTATED BAP1 WILD-TYPE
  STAGE I               8            166
  STAGE II              6             80
  STAGE III             0              3
  STAGE IIIA            1             63
  STAGE IIIB            0              9
  STAGE IIIC            2              7
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             1              1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BAP1 MUTATED     8   8   3   2
  BAP1 WILD-TYPE 176  86  76  11
D6V4, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  T1            8            176
  T2            8             86
  T3            3             76
  T4            2             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
                cls
clus               0   1
  BAP1 MUTATED    11   1
  BAP1 WILD-TYPE 243   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED     11    1
  BAP1 WILD-TYPE  243    3
   clus
vv  BAP1 MUTATED BAP1 WILD-TYPE
  0           11            243
  1            1              3
[1] 2 2
[1] FALSE
D6V6, binary
                cls
clus               0   1
  BAP1 MUTATED    12   1
  BAP1 WILD-TYPE 257   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED     12    1
  BAP1 WILD-TYPE  257    3
   clus
vv  BAP1 MUTATED BAP1 WILD-TYPE
  0           12            257
  1            1              3
[1] 2 2
[1] FALSE
D6V7, binary
                cls
clus               0   1
  BAP1 MUTATED    17   4
  BAP1 WILD-TYPE 104 248
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED     17    4
  BAP1 WILD-TYPE  104  248
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  FEMALE           17            104
  MALE              4            248
[1] 2 2
[1] FALSE
D6V8, binary
                cls
clus               0   1
  BAP1 MUTATED    19   0
  BAP1 WILD-TYPE 322   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED     19    0
  BAP1 WILD-TYPE  322    9
     clus
vv    BAP1 MUTATED BAP1 WILD-TYPE
  NO            19            322
  YES            0              9
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  BAP1 MUTATED                         0                       19
  BAP1 WILD-TYPE                       3                      344
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  BAP1 MUTATED                                  2
  BAP1 WILD-TYPE                                5
D6V9, multiclass
                                  clus
vv                                 BAP1 MUTATED BAP1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              3
  HEPATOCELLULAR CARCINOMA                   19            344
  HEPATOCHOLANGIOCARCINOMA (MIXED)            2              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BAP1 MUTATED    19   1   0   1
  BAP1 WILD-TYPE 308  15   1  21
D6V10, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  R0           19            308
  R1            1             15
  R2            0              1
  RX            1             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BAP1 MUTATED                                  0     5
  BAP1 WILD-TYPE                                2   155
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BAP1 MUTATED                           0    16
  BAP1 WILD-TYPE                        17   168
D6V11, multiclass
                                  clus
vv                                 BAP1 MUTATED BAP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       5            155
  BLACK OR AFRICAN AMERICAN                   0             17
  WHITE                                      16            168
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, binary
                cls
clus               0   1
  BAP1 MUTATED     1  20
  BAP1 WILD-TYPE  17 317
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      1   20
  BAP1 WILD-TYPE   17  317
                        clus
vv                       BAP1 MUTATED BAP1 WILD-TYPE
  HISPANIC OR LATINO                1             17
  NOT HISPANIC OR LATINO           20            317
[1] 2 2
[1] FALSE

Clustering(7) Variable = CDC27 MUTATION ANALYSIS
D7V1, survival
                 sevent
clus2               0   1
  CDC27 MUTATED    10   5
  CDC27 WILD-TYPE 227 125
  CDC27 MUTATED CDC27 WILD-TYPE 
             15             352 
  CDC27 MUTATED CDC27 WILD-TYPE 
              5             125 
$`CDC27 MUTATED`
TCGA-ES-A2HS TCGA-2Y-A9GX TCGA-BC-4073 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A1EA 
       22.62        80.28        27.91        53.33         2.60        79.40 
TCGA-DD-A1EB TCGA-DD-A1EJ TCGA-DD-A39Z TCGA-DD-AACA TCGA-DD-AADR TCGA-EP-A12J 
       66.31        33.04        19.76        75.65        66.67        18.74 
TCGA-EP-A2KA TCGA-FV-A4ZQ TCGA-G3-A3CJ 
       20.61         0.39        19.53 

$`CDC27 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 
       21.17        21.83        18.90        23.64         9.96         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       23.80        53.39        63.75        41.79        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
      120.82        40.41        56.91        49.84        47.74        18.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       20.81        22.92         1.18         8.55        13.02        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-A10Q 
       10.59         0.66        17.10        14.76         1.51        37.32 
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       10.13        27.52        27.52         2.99        25.32        23.38 
TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        1.12        44.42        45.93         0.26        22.36        14.60 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 
       18.48        44.81        13.45         0.66         4.24         8.22 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 
        2.86         3.19         3.39         4.24         3.35         7.20 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.32         9.86         9.96        10.36        11.93        11.41 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
        9.99         8.94         7.13        21.34         9.83        12.00 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT 
       13.12        12.56         8.61         9.14         9.86         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 
       11.31         9.17         6.94         8.15        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       83.57       113.00         7.33         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       90.71        19.79        75.65        11.47        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
       49.15         6.02        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.69         5.62        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ 
       32.52        21.70        30.97        26.37        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       11.41        76.41        55.40        12.53        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        40.08        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        29.52        14.89        15.06        14.33 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       25.08        26.63        25.78        50.33        35.08        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       89.69        82.62        59.93        72.39        80.71        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        60.99 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        9.73         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A26S TCGA-EP-A2KB 
       13.41        13.35         1.84         0.20        19.99        19.59 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        0.62        11.93        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25S TCGA-G3-A25T 
       27.88        12.03         0.03         0.33        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        14.86        21.53        25.64         5.92 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        25.25        22.95        24.46        20.42        17.10 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       14.70        20.78        11.87        14.14        15.78        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80        12.23        13.55         0.89        11.64         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        28.90         1.02         2.20         2.99        37.71 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06        16.83        11.80        27.25        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        26.27        17.69        21.01         3.09 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        15.52        36.10        27.88        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        1.71        15.98        10.75        11.34         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       20.22        24.85        18.28        33.86        30.41        22.78 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       13.55        35.77        25.71        23.21        35.87        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        79.30        11.21 

  CDC27 MUTATED CDC27 WILD-TYPE 
           0.39            0.03 
  CDC27 MUTATED CDC27 WILD-TYPE 
          80.28          120.82 
  CDC27 MUTATED CDC27 WILD-TYPE 
         27.910          19.315 
[1] "0.4 - 80.3 (27.9)"  "0.0 - 120.8 (19.3)"
[1] "hr=" "1.4"
D7V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CDC27 MUTATED         8        3         0          3          0          1
  CDC27 WILD-TYPE     166       83         3         61          9          8
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  CDC27 MUTATED          0         0         0
  CDC27 WILD-TYPE        2         1         2
D7V3, multiclass
            clus
vv           CDC27 MUTATED CDC27 WILD-TYPE
  STAGE I                8             166
  STAGE II               3              83
  STAGE III              0               3
  STAGE IIIA             3              61
  STAGE IIIB             0               9
  STAGE IIIC             1               8
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDC27 MUTATED     9   3   3   0
  CDC27 WILD-TYPE 175  91  76  13
D7V4, multiclass
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  T1             9             175
  T2             3              91
  T3             3              76
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
                 cls
clus                0   1
  CDC27 MUTATED     8   1
  CDC27 WILD-TYPE 246   3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      8    1
  CDC27 WILD-TYPE  246    3
   clus
vv  CDC27 MUTATED CDC27 WILD-TYPE
  0             8             246
  1             1               3
[1] 2 2
[1] FALSE
D7V6, binary
                 cls
clus                0   1
  CDC27 MUTATED    10   0
  CDC27 WILD-TYPE 259   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED     10    0
  CDC27 WILD-TYPE  259    4
   clus
vv  CDC27 MUTATED CDC27 WILD-TYPE
  0            10             259
  1             0               4
[1] 2 2
[1] FALSE
D7V7, binary
                 cls
clus                0   1
  CDC27 MUTATED     4  11
  CDC27 WILD-TYPE 117 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      4   11
  CDC27 WILD-TYPE  117  241
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  FEMALE             4             117
  MALE              11             241
[1] 2 2
[1] FALSE
D7V8, binary
                 cls
clus                0   1
  CDC27 MUTATED    10   1
  CDC27 WILD-TYPE 331   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED     10    1
  CDC27 WILD-TYPE  331    8
     clus
vv    CDC27 MUTATED CDC27 WILD-TYPE
  NO             10             331
  YES             1               8
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  CDC27 MUTATED                         0                       15
  CDC27 WILD-TYPE                       3                      348
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  CDC27 MUTATED                                  0
  CDC27 WILD-TYPE                                7
D7V9, multiclass
                                  clus
vv                                 CDC27 MUTATED CDC27 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                    15             348
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CDC27 MUTATED    13   2   0   0
  CDC27 WILD-TYPE 314  14   1  22
D7V10, multiclass
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  R0            13             314
  R1             2              14
  R2             0               1
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDC27 MUTATED                                  1     4
  CDC27 WILD-TYPE                                1   156
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDC27 MUTATED                           2     6
  CDC27 WILD-TYPE                        15   178
D7V11, multiclass
                                  clus
vv                                 CDC27 MUTATED CDC27 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               1
  ASIAN                                        4             156
  BLACK OR AFRICAN AMERICAN                    2              15
  WHITE                                        6             178
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, binary
                 cls
clus                0   1
  CDC27 MUTATED     0  13
  CDC27 WILD-TYPE  18 324
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      0   13
  CDC27 WILD-TYPE   18  324
                        clus
vv                       CDC27 MUTATED CDC27 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO            13             324
[1] 2 2
[1] FALSE

Clustering(8) Variable = CDKN2A MUTATION ANALYSIS
D8V1, survival
                  sevent
clus2                0   1
  CDKN2A MUTATED    10   1
  CDKN2A WILD-TYPE 227 129
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              11              356 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               1              129 
$`CDKN2A MUTATED`
TCGA-XR-A8TG TCGA-DD-AAC9 TCGA-DD-AACK TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       29.52        11.41         0.30        44.22        22.09        40.08 
TCGA-DD-AADG TCGA-DD-AADM TCGA-DD-AAW3 TCGA-ED-A7XP TCGA-G3-AAV0 
       37.64         0.39        53.69        13.15        15.65 

$`CDKN2A WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        0.76         7.04        10.32        44.02         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        20.81        22.92         1.18         8.55        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        17.10        14.76         1.51 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        14.60        18.48        44.81        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.24         8.22         2.86         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.35         7.20         3.32         9.86         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
       11.93        11.41         9.99         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        9.83        12.00        13.12        12.56         8.61         9.14 
TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.86         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65        11.47        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       27.19        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       30.61        33.14        32.52        21.70        30.97        26.37 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
       13.48         0.53        75.65        76.41        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       71.80        12.00        15.42         6.41        53.19        69.11 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       40.54        40.83        13.97        40.47        39.52         3.78 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO 
       35.67        35.05        34.49        20.91        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        23.74        15.72        25.08        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        90.48        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.39        80.71        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       66.25        65.39        60.99        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       14.04        13.41        13.35         1.84         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       19.99        20.61        19.59         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       25.25        22.95        24.46        20.42        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 
       20.78        11.87        14.14        15.78        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
            0.30             0.03 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           53.69           120.82 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           22.09            19.76 
[1] "0.3 - 53.7 (22.1)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "3.6"
D8V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CDKN2A MUTATED         7        2         0          2          0          0
  CDKN2A WILD-TYPE     167       84         3         62          9          9
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  CDKN2A MUTATED          0         0         0
  CDKN2A WILD-TYPE        2         1         2
D8V3, multiclass
            clus
vv           CDKN2A MUTATED CDKN2A WILD-TYPE
  STAGE I                 7              167
  STAGE II                2               84
  STAGE III               0                3
  STAGE IIIA              2               62
  STAGE IIIB              0                9
  STAGE IIIC              0                9
  STAGE IV                0                2
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CDKN2A MUTATED     7   2   2   0
  CDKN2A WILD-TYPE 177  92  77  13
D8V4, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  T1              7              177
  T2              2               92
  T3              2               77
  T4              0               13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    10   0
  CDKN2A WILD-TYPE 244   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     10    0
  CDKN2A WILD-TYPE  244    4
   clus
vv  CDKN2A MUTATED CDKN2A WILD-TYPE
  0             10              244
  1              0                4
[1] 2 2
[1] FALSE
D8V6, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    11   0
  CDKN2A WILD-TYPE 258   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     11    0
  CDKN2A WILD-TYPE  258    4
   clus
vv  CDKN2A MUTATED CDKN2A WILD-TYPE
  0             11              258
  1              0                4
[1] 2 2
[1] FALSE
D8V7, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     2   9
  CDKN2A WILD-TYPE 119 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      2    9
  CDKN2A WILD-TYPE  119  243
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE              2              119
  MALE                9              243
[1] 2 2
[1] FALSE
D8V8, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    10   1
  CDKN2A WILD-TYPE 331   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     10    1
  CDKN2A WILD-TYPE  331    8
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  NO              10              331
  YES              1                8
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  CDKN2A MUTATED                         0                       11
  CDKN2A WILD-TYPE                       3                      352
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  CDKN2A MUTATED                                  0
  CDKN2A WILD-TYPE                                7
D8V9, multiclass
                                  clus
vv                                 CDKN2A MUTATED CDKN2A WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                3
  HEPATOCELLULAR CARCINOMA                     11              352
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CDKN2A MUTATED    11   0   0   0
  CDKN2A WILD-TYPE 316  16   1  22
D8V10, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  R0             11              316
  R1              0               16
  R2              0                1
  RX              0               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDKN2A MUTATED                                  0    10
  CDKN2A WILD-TYPE                                2   150
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CDKN2A MUTATED                           0     1
  CDKN2A WILD-TYPE                        17   183
D8V11, multiclass
                                  clus
vv                                 CDKN2A MUTATED CDKN2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                        10              150
  BLACK OR AFRICAN AMERICAN                     0               17
  WHITE                                         1              183
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     1  10
  CDKN2A WILD-TYPE  17 327
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      1   10
  CDKN2A WILD-TYPE   17  327
                        clus
vv                       CDKN2A MUTATED CDKN2A WILD-TYPE
  HISPANIC OR LATINO                  1               17
  NOT HISPANIC OR LATINO             10              327
[1] 2 2
[1] FALSE

Clustering(9) Variable = KRT2 MUTATION ANALYSIS
D9V1, survival
                sevent
clus2              0   1
  KRT2 MUTATED     8   4
  KRT2 WILD-TYPE 229 126
  KRT2 MUTATED KRT2 WILD-TYPE 
            12            355 
  KRT2 MUTATED KRT2 WILD-TYPE 
             4            126 
$`KRT2 MUTATED`
TCGA-4R-AA8I TCGA-BD-A3ER TCGA-2Y-A9GU TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A4NJ 
        8.61        36.66        63.75        27.19        55.69        30.51 
TCGA-DD-AA3A TCGA-DD-AAD0 TCGA-DD-AADD TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVS 
       13.48         4.50        40.47        35.08        89.69        59.93 

$`KRT2 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        11.74        38.40        69.57         5.03        17.98 
TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 TCGA-DD-AAE8 
        0.36        90.28        26.83        18.87        21.17        21.83 
TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 
       18.90        23.64         9.96        22.62         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
       81.73        30.74        22.13        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
        2.14        31.27        12.72        24.56         0.76         7.04 
TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
       10.32        44.02        29.52         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       53.39        41.79        80.28        24.89        27.88       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 
       40.41        56.91        49.84        47.74        18.25        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH 
       22.92         1.18         8.55        13.02        10.78        10.59 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q 
        0.66        17.10        14.76         1.51        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       10.13        27.52        27.52         2.99        25.32        23.38 
TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        1.12        44.42        45.93         0.26        22.36        14.60 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 
       18.48        44.81        13.45         0.66         4.24         8.22 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 
        2.86         3.19         3.39         4.24         3.35         7.20 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.32         9.86         9.96        10.36        11.93        11.41 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
        9.99         8.94         7.13        21.34         9.83        12.00 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT 
       13.12        12.56         8.61         9.14         9.86         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 
       11.31         9.17         6.94         8.15        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65        11.47        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z 
       33.04        18.35        13.64        21.14         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE 
      107.11        13.78        30.61        33.14        32.52        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.97        26.37        30.15        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
      114.35         0.53        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        71.80        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       69.11         0.30         3.52        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV 
       13.64        14.20        59.31        51.35        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 
       46.82         5.59        47.67         5.62        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       13.97        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       34.49        20.91         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
       14.33        66.67        15.58        18.21        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAVP TCGA-DD-AAVR TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       90.48        82.62        72.39        80.71        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       64.77        62.47        66.25        65.39        60.99        53.69 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       29.92        26.93        28.08        13.91        13.35         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20        12.82         0.20        14.04        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.35         1.84         0.20        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       19.59         0.62        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
       19.10        27.88        12.03         0.03         0.33         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z 
       13.68        51.06        53.79        28.27        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        25.25        22.95 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       24.46        20.42        17.10        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        0.89        11.64         2.14        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       27.25        29.79        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       22.95        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       17.69        21.01         3.09         0.72         0.49         0.30 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.04        19.33        19.04        15.39        15.52        36.10 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       27.88        19.76        16.44         1.71        15.98        10.75 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       11.34         0.99        12.99        20.22        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        22.78        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.21        35.87        25.15        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  KRT2 MUTATED KRT2 WILD-TYPE 
          4.50           0.03 
  KRT2 MUTATED KRT2 WILD-TYPE 
         89.69         120.82 
  KRT2 MUTATED KRT2 WILD-TYPE 
         35.87          19.53 
[1] "4.5 - 89.7 (35.9)"  "0.0 - 120.8 (19.5)"
[1] "hr=" "1.5"
D9V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  KRT2 MUTATED         7        4         1          0          0          0
  KRT2 WILD-TYPE     167       82         2         64          9          9
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  KRT2 MUTATED          0         0         0
  KRT2 WILD-TYPE        2         1         2
D9V3, multiclass
            clus
vv           KRT2 MUTATED KRT2 WILD-TYPE
  STAGE I               7            167
  STAGE II              4             82
  STAGE III             1              2
  STAGE IIIA            0             64
  STAGE IIIB            0              9
  STAGE IIIC            0              9
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KRT2 MUTATED     7   4   1   0
  KRT2 WILD-TYPE 177  90  78  13
D9V4, multiclass
    clus
vv   KRT2 MUTATED KRT2 WILD-TYPE
  T1            7            177
  T2            4             90
  T3            1             78
  T4            0             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
                cls
clus               0   1
  KRT2 MUTATED     8   0
  KRT2 WILD-TYPE 246   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED      8    0
  KRT2 WILD-TYPE  246    4
   clus
vv  KRT2 MUTATED KRT2 WILD-TYPE
  0            8            246
  1            0              4
[1] 2 2
[1] FALSE
D9V6, binary
                cls
clus               0   1
  KRT2 MUTATED     8   0
  KRT2 WILD-TYPE 261   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED      8    0
  KRT2 WILD-TYPE  261    4
   clus
vv  KRT2 MUTATED KRT2 WILD-TYPE
  0            8            261
  1            0              4
[1] 2 2
[1] FALSE
D9V7, binary
                cls
clus               0   1
  KRT2 MUTATED     6   6
  KRT2 WILD-TYPE 115 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED      6    6
  KRT2 WILD-TYPE  115  246
        clus
vv       KRT2 MUTATED KRT2 WILD-TYPE
  FEMALE            6            115
  MALE              6            246
[1] 2 2
[1] FALSE
D9V8, binary
                cls
clus               0   1
  KRT2 MUTATED    11   0
  KRT2 WILD-TYPE 330   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED     11    0
  KRT2 WILD-TYPE  330    9
     clus
vv    KRT2 MUTATED KRT2 WILD-TYPE
  NO            11            330
  YES            0              9
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  KRT2 MUTATED                         0                       11
  KRT2 WILD-TYPE                       3                      352
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  KRT2 MUTATED                                  1
  KRT2 WILD-TYPE                                6
D9V9, multiclass
                                  clus
vv                                 KRT2 MUTATED KRT2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              3
  HEPATOCELLULAR CARCINOMA                   11            352
  HEPATOCHOLANGIOCARCINOMA (MIXED)            1              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  KRT2 MUTATED    12   0   0   0
  KRT2 WILD-TYPE 315  16   1  22
D9V10, multiclass
    clus
vv   KRT2 MUTATED KRT2 WILD-TYPE
  R0           12            315
  R1            0             16
  R2            0              1
  RX            0             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRT2 MUTATED                                  0     5
  KRT2 WILD-TYPE                                2   155
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KRT2 MUTATED                           0     7
  KRT2 WILD-TYPE                        17   177
D9V11, multiclass
                                  clus
vv                                 KRT2 MUTATED KRT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       5            155
  BLACK OR AFRICAN AMERICAN                   0             17
  WHITE                                       7            177
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, binary
                cls
clus               0   1
  KRT2 MUTATED     0  12
  KRT2 WILD-TYPE  18 325
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED      0   12
  KRT2 WILD-TYPE   18  325
                        clus
vv                       KRT2 MUTATED KRT2 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO           12            325
[1] 2 2
[1] FALSE

Clustering(10) Variable = NFE2L2 MUTATION ANALYSIS
D10V1, survival
                  sevent
clus2                0   1
  NFE2L2 MUTATED     8   5
  NFE2L2 WILD-TYPE 229 125
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              13              354 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               5              125 
$`NFE2L2 MUTATED`
TCGA-DD-A4NI TCGA-FV-A3I1 TCGA-5R-AAAM TCGA-DD-A1EE TCGA-DD-A39V TCGA-DD-A4NO 
       26.83         8.12         1.51        11.47        21.14        73.81 
TCGA-DD-AAC8 TCGA-DD-AADJ TCGA-DD-AAEH TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVY 
        0.53        35.05        25.78        59.93        72.39        64.77 
TCGA-G3-AAV3 
       13.55 

$`NFE2L2 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAE7 
       17.98        36.66         0.36        90.28        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3R2 
       21.83        18.90        23.64         9.96        22.62         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
       81.73        30.74        22.13        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
        2.14        31.27        12.72        24.56         0.76         7.04 
TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
       10.32        44.02        29.52         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
      120.82        40.41        56.91        49.84        47.74        18.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       20.81        22.92         1.18         8.55        13.02        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-BC-4073 TCGA-BC-A10Q 
       10.59         0.66        17.10        14.76        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       10.13        27.52        27.52         2.99        25.32        23.38 
TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        1.12        44.42        45.93         0.26        22.36        14.60 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 
       18.48        44.81        13.45         0.66         4.24         8.22 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 
        2.86         3.19         3.39         4.24         3.35         7.20 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.32         9.86         9.96        10.36        11.93        11.41 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
        9.99         8.94         7.13        21.34         9.83        12.00 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT 
       13.12        12.56         8.61         9.14         9.86         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 
       11.31         9.17         6.94         8.15        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        12.95        45.11        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       18.35        13.64        27.19        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE 
      107.11        13.78        30.61        33.14        32.52        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        26.37        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
      114.35        13.48        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        71.80        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       69.11         0.30         3.52        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV 
       13.64        14.20        59.31        51.35        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       46.82         5.59        47.67         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        42.58        44.22        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.83        13.97        40.47        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.67        34.49        20.91         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEI 
        4.64        23.74        15.72        25.08        26.63        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVV TCGA-DD-AAVW 
       35.08        90.48        89.69        82.62        80.71        76.18 
TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       56.48        62.47        66.25        65.39        60.99        53.69 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       29.92        26.93        28.08        13.91        13.35         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20        12.82         0.20        14.04        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.35         1.84         0.20        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       19.59         0.62        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
       19.10        27.88        12.03         0.03         0.33         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z 
       13.68        51.06        53.79        28.27        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        25.25        22.95 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       24.46        20.42        17.10        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV4 
       14.14        15.78        15.65        11.80        12.23         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       11.64         2.14        11.87        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 
        2.99        37.71        17.06        16.83        11.80        27.25 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       29.79        13.97        12.03         9.57        16.67        22.95 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         7.53        10.85        58.88        26.27        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 
       21.01         3.09         0.72         0.49         0.30        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       19.33        19.04        15.39        15.52        36.10        27.88 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L 
       19.76        16.44         1.71        15.98        10.75        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD 
        0.99        12.99        20.22        24.85        18.28        33.86 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       30.41        22.78        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.87        25.15        12.99        45.57        79.30        11.21 

  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
            0.53             0.03 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           73.81           120.82 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
          25.780           19.675 
[1] "0.5 - 73.8 (25.8)"  "0.0 - 120.8 (19.7)"
[1] "hr=" "1"  
D10V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  NFE2L2 MUTATED         5        6         0          2          0          0
  NFE2L2 WILD-TYPE     169       80         3         62          9          9
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  NFE2L2 MUTATED          0         0         0
  NFE2L2 WILD-TYPE        2         1         2
D10V3, multiclass
            clus
vv           NFE2L2 MUTATED NFE2L2 WILD-TYPE
  STAGE I                 5              169
  STAGE II                6               80
  STAGE III               0                3
  STAGE IIIA              2               62
  STAGE IIIB              0                9
  STAGE IIIC              0                9
  STAGE IV                0                2
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NFE2L2 MUTATED     5   6   2   0
  NFE2L2 WILD-TYPE 179  88  77  13
D10V4, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  T1              5              179
  T2              6               88
  T3              2               77
  T4              0               13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED    11   0
  NFE2L2 WILD-TYPE 243   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED     11    0
  NFE2L2 WILD-TYPE  243    4
   clus
vv  NFE2L2 MUTATED NFE2L2 WILD-TYPE
  0             11              243
  1              0                4
[1] 2 2
[1] FALSE
D10V6, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED    12   0
  NFE2L2 WILD-TYPE 257   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED     12    0
  NFE2L2 WILD-TYPE  257    4
   clus
vv  NFE2L2 MUTATED NFE2L2 WILD-TYPE
  0             12              257
  1              0                4
[1] 2 2
[1] FALSE
D10V7, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     4   9
  NFE2L2 WILD-TYPE 117 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      4    9
  NFE2L2 WILD-TYPE  117  243
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  FEMALE              4              117
  MALE                9              243
[1] 2 2
[1] FALSE
D10V8, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED    12   1
  NFE2L2 WILD-TYPE 329   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED     12    1
  NFE2L2 WILD-TYPE  329    8
     clus
vv    NFE2L2 MUTATED NFE2L2 WILD-TYPE
  NO              12              329
  YES              1                8
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  NFE2L2 MUTATED                         0                       13
  NFE2L2 WILD-TYPE                       3                      350
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  NFE2L2 MUTATED                                  0
  NFE2L2 WILD-TYPE                                7
D10V9, multiclass
                                  clus
vv                                 NFE2L2 MUTATED NFE2L2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                3
  HEPATOCELLULAR CARCINOMA                     13              350
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NFE2L2 MUTATED    13   0   0   0
  NFE2L2 WILD-TYPE 314  16   1  22
D10V10, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  R0             13              314
  R1              0               16
  R2              0                1
  RX              0               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NFE2L2 MUTATED                                  0     6
  NFE2L2 WILD-TYPE                                2   154
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NFE2L2 MUTATED                           0     7
  NFE2L2 WILD-TYPE                        17   177
D10V11, multiclass
                                  clus
vv                                 NFE2L2 MUTATED NFE2L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         6              154
  BLACK OR AFRICAN AMERICAN                     0               17
  WHITE                                         7              177
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     0  13
  NFE2L2 WILD-TYPE  18 324
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      0   13
  NFE2L2 WILD-TYPE   18  324
                        clus
vv                       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO             13              324
[1] 2 2
[1] FALSE

Clustering(11) Variable = PTEN MUTATION ANALYSIS
D11V1, survival
                sevent
clus2              0   1
  PTEN MUTATED     7   4
  PTEN WILD-TYPE 230 126
  PTEN MUTATED PTEN WILD-TYPE 
            11            356 
  PTEN MUTATED PTEN WILD-TYPE 
             4            126 
$`PTEN MUTATED`
TCGA-BC-A112 TCGA-G3-A6UC TCGA-BC-A3KF TCGA-BD-A2L6 TCGA-CC-A5UD TCGA-DD-A3A0 
        5.03        22.06         0.26        44.81         9.99        25.81 
TCGA-DD-A4NE TCGA-DD-AAD0 TCGA-DD-AAE2 TCGA-DD-AAW3 TCGA-QA-A7B7 
       21.70         4.50        20.98        53.69         3.09 

$`PTEN WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A7M9 TCGA-K7-A5RF 
        6.38        81.73        30.74        22.13         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
        2.14        31.27        12.72        24.56         0.76         7.04 
TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
       10.32        44.02        29.52         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
      120.82        40.41        56.91        49.84        47.74        18.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       20.81        22.92         1.18         8.55        13.02        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 
       10.59         0.66        17.10        14.76         1.51        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H 
       23.38         1.12        44.42        45.93        22.36        14.60 
TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 
       18.48        13.45         0.66         4.24         8.22         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT 
        3.19         3.39         4.24         3.35         7.20         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE 
        9.86         9.96        10.36        11.93        11.41         8.94 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ 
        7.13        21.34         9.83        12.00        13.12        12.56 
TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
        8.61         9.14         9.86         4.60        11.31         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        6.94         8.15        79.73        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
      113.00         7.33         2.60         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65        11.47 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        33.04        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       13.64        21.14        27.19        55.69         5.62        19.76 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NG 
       13.78        30.61        33.14        32.52        30.97        26.37 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        71.80        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       69.11         0.30         3.52        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV 
       13.64        14.20        59.31        51.35        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 
       46.82         5.59        47.67         5.62        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.05        34.49        20.91         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.25        18.15        18.61        19.99         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        89.69        82.62        59.93        72.39 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       65.39        60.99        29.92        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         9.73         0.20        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       13.15        13.41        13.35         1.84         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       19.99        20.61        19.59         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       25.25        22.95        24.46        20.42        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       20.78        11.87        14.14        15.78        15.65        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       12.23        13.55         0.89        11.64         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A6M4 TCGA-RC-A6M5 
       58.88        26.27        17.69        21.01         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  PTEN MUTATED PTEN WILD-TYPE 
          0.26           0.03 
  PTEN MUTATED PTEN WILD-TYPE 
         53.69         120.82 
  PTEN MUTATED PTEN WILD-TYPE 
         20.98          19.76 
[1] "0.3 - 53.7 (21.0)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.4"
D11V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PTEN MUTATED         5        1         0          2          1          0
  PTEN WILD-TYPE     169       85         3         62          8          9
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  PTEN MUTATED          0         0         0
  PTEN WILD-TYPE        2         1         2
D11V3, multiclass
            clus
vv           PTEN MUTATED PTEN WILD-TYPE
  STAGE I               5            169
  STAGE II              1             85
  STAGE III             0              3
  STAGE IIIA            2             62
  STAGE IIIB            1              8
  STAGE IIIC            0              9
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PTEN MUTATED     5   2   4   0
  PTEN WILD-TYPE 179  92  75  13
D11V4, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  T1            5            179
  T2            2             92
  T3            4             75
  T4            0             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V5, binary
                cls
clus               0   1
  PTEN MUTATED     6   0
  PTEN WILD-TYPE 248   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      6    0
  PTEN WILD-TYPE  248    4
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0            6            248
  1            0              4
[1] 2 2
[1] FALSE
D11V6, binary
                cls
clus               0   1
  PTEN MUTATED     8   0
  PTEN WILD-TYPE 261   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      8    0
  PTEN WILD-TYPE  261    4
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0            8            261
  1            0              4
[1] 2 2
[1] FALSE
D11V7, binary
                cls
clus               0   1
  PTEN MUTATED     3   8
  PTEN WILD-TYPE 118 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      3    8
  PTEN WILD-TYPE  118  244
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            3            118
  MALE              8            244
[1] 2 2
[1] FALSE
D11V8, binary
                cls
clus               0   1
  PTEN MUTATED    10   0
  PTEN WILD-TYPE 331   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     10    0
  PTEN WILD-TYPE  331    9
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO            10            331
  YES            0              9
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  PTEN MUTATED                         0                       11
  PTEN WILD-TYPE                       3                      352
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  PTEN MUTATED                                  0
  PTEN WILD-TYPE                                7
D11V9, multiclass
                                  clus
vv                                 PTEN MUTATED PTEN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              3
  HEPATOCELLULAR CARCINOMA                   11            352
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PTEN MUTATED    10   0   0   1
  PTEN WILD-TYPE 317  16   1  21
D11V10, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  R0           10            317
  R1            0             16
  R2            0              1
  RX            1             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTEN MUTATED                                  0     4
  PTEN WILD-TYPE                                2   156
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED                           1     6
  PTEN WILD-TYPE                        16   178
D11V11, multiclass
                                  clus
vv                                 PTEN MUTATED PTEN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       4            156
  BLACK OR AFRICAN AMERICAN                   1             16
  WHITE                                       6            178
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V12, binary
                cls
clus               0   1
  PTEN MUTATED     1   8
  PTEN WILD-TYPE  17 329
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      1    8
  PTEN WILD-TYPE   17  329
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                1             17
  NOT HISPANIC OR LATINO            8            329
[1] 2 2
[1] FALSE

Clustering(12) Variable = ARID2 MUTATION ANALYSIS
D12V1, survival
                 sevent
clus2               0   1
  ARID2 MUTATED    12  10
  ARID2 WILD-TYPE 225 120
  ARID2 MUTATED ARID2 WILD-TYPE 
             22             345 
  ARID2 MUTATED ARID2 WILD-TYPE 
             10             120 
$`ARID2 MUTATED`
TCGA-BC-A112 TCGA-3K-AAZ8 TCGA-CC-A3MA TCGA-CC-A7IE TCGA-CC-A8HT TCGA-DD-A3A0 
        5.03        13.02         9.96         7.13         4.60        25.81 
TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-AAC8 TCGA-DD-AACD TCGA-DD-AADI TCGA-DD-AAEH 
        9.30        22.78         0.53        12.53        35.67        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-AAV4 TCGA-MI-A75C 
       50.33        35.08        24.46        20.42         0.89         9.57 
TCGA-RC-A7SH TCGA-UB-AA0U TCGA-XR-A8TD TCGA-ZP-A9CV 
       15.39        10.75        33.86        35.77 

$`ARID2 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-5C-A9VG 
       18.25        20.81        22.92         1.18         8.55        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 
       10.59         0.66        17.10        14.76         1.51        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.38         1.12        44.42        45.93         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       14.60        18.48        44.81        13.45         0.66         4.24 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
        8.22         2.86         3.19         3.39         4.24         3.35 
TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        7.20         3.32         9.86        10.36        11.93        11.41 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II 
        9.99         8.94        21.34         9.83        12.00        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HU TCGA-CC-A8HV 
       12.56         8.61         9.14         9.86        11.31         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        6.94         8.15        79.73        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
      113.00         7.33         2.60         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65        11.47 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        33.04        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       13.64        21.14        27.19        55.69         5.62        19.76 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF 
       13.78        30.61        33.14        32.52        21.70        30.97 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       26.37        30.15        30.51        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       23.93        23.05         1.45        35.67       114.35        13.48 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF 
       11.41        75.65        76.41        55.40        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        40.08        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
       39.52         3.78        37.64        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
        0.39        29.52        14.89        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       25.08        26.63        90.48        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.39        80.71        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        60.99        53.69        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       28.08        13.91        13.35         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20        14.04        13.15        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        20.61        19.59         0.62 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A7M5 
       19.53        19.23        25.25        22.95        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       20.78        11.87        14.14        15.78        15.65        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       12.23        13.55        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75E 
       11.80        27.25        29.79        13.97        12.03        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       22.95        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       17.69        21.01         3.09         0.72         0.49         0.30 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       21.04        19.33        19.04        15.52        36.10        27.88 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-WJ-A86L TCGA-WQ-A9G7 
       19.76        16.44         1.71        15.98        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TE TCGA-XR-A8TF 
       12.99        20.22        24.85        18.28        30.41        22.78 
TCGA-YA-A8S7 TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       13.55        25.71        23.21        35.87        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  ARID2 MUTATED ARID2 WILD-TYPE 
           0.53            0.03 
  ARID2 MUTATED ARID2 WILD-TYPE 
          50.33          120.82 
  ARID2 MUTATED ARID2 WILD-TYPE 
         14.205          19.790 
[1] "0.5 - 50.3 (14.2)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.8"
D12V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ARID2 MUTATED        10        5         0          3          2          0
  ARID2 WILD-TYPE     164       81         3         61          7          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  ARID2 MUTATED          0         0         0
  ARID2 WILD-TYPE        2         1         2
D12V3, multiclass
            clus
vv           ARID2 MUTATED ARID2 WILD-TYPE
  STAGE I               10             164
  STAGE II               5              81
  STAGE III              0               3
  STAGE IIIA             3              61
  STAGE IIIB             2               7
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ARID2 MUTATED    11   5   6   0
  ARID2 WILD-TYPE 173  89  73  13
D12V4, multiclass
    clus
vv   ARID2 MUTATED ARID2 WILD-TYPE
  T1            11             173
  T2             5              89
  T3             6              73
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V5, binary
                 cls
clus                0   1
  ARID2 MUTATED    14   0
  ARID2 WILD-TYPE 240   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     14    0
  ARID2 WILD-TYPE  240    4
   clus
vv  ARID2 MUTATED ARID2 WILD-TYPE
  0            14             240
  1             0               4
[1] 2 2
[1] FALSE
D12V6, binary
                 cls
clus                0   1
  ARID2 MUTATED    17   0
  ARID2 WILD-TYPE 252   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     17    0
  ARID2 WILD-TYPE  252    4
   clus
vv  ARID2 MUTATED ARID2 WILD-TYPE
  0            17             252
  1             0               4
[1] 2 2
[1] FALSE
D12V7, binary
                 cls
clus                0   1
  ARID2 MUTATED     5  17
  ARID2 WILD-TYPE 116 235
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED      5   17
  ARID2 WILD-TYPE  116  235
        clus
vv       ARID2 MUTATED ARID2 WILD-TYPE
  FEMALE             5             116
  MALE              17             235
[1] 2 2
[1] FALSE
D12V8, binary
                 cls
clus                0   1
  ARID2 MUTATED    22   0
  ARID2 WILD-TYPE 319   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     22    0
  ARID2 WILD-TYPE  319    9
     clus
vv    ARID2 MUTATED ARID2 WILD-TYPE
  NO             22             319
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  ARID2 MUTATED                         0                       22
  ARID2 WILD-TYPE                       3                      341
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  ARID2 MUTATED                                  0
  ARID2 WILD-TYPE                                7
D12V9, multiclass
                                  clus
vv                                 ARID2 MUTATED ARID2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                    22             341
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ARID2 MUTATED    20   1   0   1
  ARID2 WILD-TYPE 307  15   1  21
D12V10, multiclass
    clus
vv   ARID2 MUTATED ARID2 WILD-TYPE
  R0            20             307
  R1             1              15
  R2             0               1
  RX             1              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID2 MUTATED                                  0    10
  ARID2 WILD-TYPE                                2   150
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ARID2 MUTATED                           1    11
  ARID2 WILD-TYPE                        16   173
D12V11, multiclass
                                  clus
vv                                 ARID2 MUTATED ARID2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                       10             150
  BLACK OR AFRICAN AMERICAN                    1              16
  WHITE                                       11             173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V12, binary
                 cls
clus                0   1
  ARID2 MUTATED     2  20
  ARID2 WILD-TYPE  16 317
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED      2   20
  ARID2 WILD-TYPE   16  317
                        clus
vv                       ARID2 MUTATED ARID2 WILD-TYPE
  HISPANIC OR LATINO                 2              16
  NOT HISPANIC OR LATINO            20             317
[1] 2 2
[1] FALSE

Clustering(13) Variable = RBM10 MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2               0   1
  RBM10 MUTATED     4   4
  RBM10 WILD-TYPE 233 126
  RBM10 MUTATED RBM10 WILD-TYPE 
              8             359 
  RBM10 MUTATED RBM10 WILD-TYPE 
              4             126 
$`RBM10 MUTATED`
TCGA-ES-A2HS TCGA-XR-A8TC TCGA-2Y-A9GZ TCGA-DD-A39Y TCGA-DD-AACO TCGA-DD-AADM 
       22.62        44.02        27.88         5.62        61.68         0.39 
TCGA-DD-AAVV TCGA-LG-A9QD 
       80.71        12.03 

$`RBM10 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 
       21.17        21.83        18.90        23.64         9.96         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
        7.04        10.32        29.52         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H0 
       53.39        63.75        41.79        80.28        24.89       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 
       40.41        56.91        49.84        47.74        18.25        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH 
       22.92         1.18         8.55        13.02        10.78        10.59 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q 
        0.66        17.10        14.76         1.51        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       10.13        27.52        27.52         2.99        25.32        23.38 
TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        1.12        44.42        45.93         0.26        22.36        14.60 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 
       18.48        44.81        13.45         0.66         4.24         8.22 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 
        2.86         3.19         3.39         4.24         3.35         7.20 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.32         9.86         9.96        10.36        11.93        11.41 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
        9.99         8.94         7.13        21.34         9.83        12.00 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT 
       13.12        12.56         8.61         9.14         9.86         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 
       11.31         9.17         6.94         8.15        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65        11.47        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       21.70        30.97        26.37        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       58.16        42.81        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       29.52        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.21        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
       18.61        19.99         4.64        23.74        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       26.63        25.78        50.33        35.08        90.48        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       82.62        59.93        72.39        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        60.99        53.69        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       26.93        28.08        13.91        13.35         9.73         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
       12.82         0.20        14.04        13.15        13.41        13.35 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        1.84         0.20        18.74        19.99        20.61        19.59 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        0.62        11.93        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S 
       27.88        12.03         0.03         0.33         0.39        13.68 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       51.06        53.79        28.27        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
        5.92        19.53        19.23        25.25        22.95        24.46 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       20.42        17.10        14.70        20.78        11.87        14.14 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       15.78        15.65        11.80        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       11.64         2.14        11.87        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 
        2.99        37.71        17.06        16.83        11.80        27.25 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       29.79        13.97         9.57        16.67        22.95        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        7.53        10.85        58.88        26.27        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB 
        3.09         0.72         0.49         0.30        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.04        15.39        15.52        36.10        27.88        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 
       16.44         1.71        15.98        10.75        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE 
       12.99        20.22        24.85        18.28        33.86        30.41 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       22.78        13.55        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        79.30        11.21 

  RBM10 MUTATED RBM10 WILD-TYPE 
           0.39            0.03 
  RBM10 MUTATED RBM10 WILD-TYPE 
          80.71          120.82 
  RBM10 MUTATED RBM10 WILD-TYPE 
          25.25           19.76 
[1] "0.4 - 80.7 (25.2)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.3"
D13V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  RBM10 MUTATED         4        3         0          1          0          0
  RBM10 WILD-TYPE     170       83         3         63          9          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  RBM10 MUTATED          0         0         0
  RBM10 WILD-TYPE        2         1         2
D13V3, multiclass
            clus
vv           RBM10 MUTATED RBM10 WILD-TYPE
  STAGE I                4             170
  STAGE II               3              83
  STAGE III              0               3
  STAGE IIIA             1              63
  STAGE IIIB             0               9
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RBM10 MUTATED     4   3   1   0
  RBM10 WILD-TYPE 180  91  78  13
D13V4, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  T1             4             180
  T2             3              91
  T3             1              78
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V5, binary
                 cls
clus                0   1
  RBM10 MUTATED     4   0
  RBM10 WILD-TYPE 250   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      4    0
  RBM10 WILD-TYPE  250    4
   clus
vv  RBM10 MUTATED RBM10 WILD-TYPE
  0             4             250
  1             0               4
[1] 2 2
[1] FALSE
D13V6, binary
                 cls
clus                0   1
  RBM10 MUTATED     5   0
  RBM10 WILD-TYPE 264   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      5    0
  RBM10 WILD-TYPE  264    4
   clus
vv  RBM10 MUTATED RBM10 WILD-TYPE
  0             5             264
  1             0               4
[1] 2 2
[1] FALSE
D13V7, binary
                 cls
clus                0   1
  RBM10 MUTATED     2   6
  RBM10 WILD-TYPE 119 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      2    6
  RBM10 WILD-TYPE  119  246
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  FEMALE             2             119
  MALE               6             246
[1] 2 2
[1] FALSE
D13V8, binary
                 cls
clus                0   1
  RBM10 MUTATED     7   0
  RBM10 WILD-TYPE 334   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      7    0
  RBM10 WILD-TYPE  334    9
     clus
vv    RBM10 MUTATED RBM10 WILD-TYPE
  NO              7             334
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  RBM10 MUTATED                         0                        8
  RBM10 WILD-TYPE                       3                      355
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  RBM10 MUTATED                                  0
  RBM10 WILD-TYPE                                7
D13V9, multiclass
                                  clus
vv                                 RBM10 MUTATED RBM10 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                     8             355
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RBM10 MUTATED     8   0   0   0
  RBM10 WILD-TYPE 319  16   1  22
D13V10, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  R0             8             319
  R1             0              16
  R2             0               1
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBM10 MUTATED                                  0     4
  RBM10 WILD-TYPE                                2   156
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RBM10 MUTATED                           0     4
  RBM10 WILD-TYPE                        17   180
D13V11, multiclass
                                  clus
vv                                 RBM10 MUTATED RBM10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        4             156
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        4             180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V12, binary
                 cls
clus                0   1
  RBM10 MUTATED     2   6
  RBM10 WILD-TYPE  16 331
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      2    6
  RBM10 WILD-TYPE   16  331
                        clus
vv                       RBM10 MUTATED RBM10 WILD-TYPE
  HISPANIC OR LATINO                 2              16
  NOT HISPANIC OR LATINO             6             331
[1] 2 2
[1] FALSE

Clustering(14) Variable = ZNF512B MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  ZNF512B MUTATED     4   4
  ZNF512B WILD-TYPE 233 126
  ZNF512B MUTATED ZNF512B WILD-TYPE 
                8               359 
  ZNF512B MUTATED ZNF512B WILD-TYPE 
                4               126 
$`ZNF512B MUTATED`
TCGA-FV-A4ZP TCGA-2Y-A9H1 TCGA-BC-A3KG TCGA-BD-A3EP TCGA-DD-A4NE TCGA-DD-AACT 
       81.73        40.41        22.36        13.45        21.70        51.35 
TCGA-FV-A4ZQ TCGA-GJ-A6C0 
        0.39         1.02 

$`ZNF512B WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        8.12         6.38        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
       27.88       120.82        56.91        49.84        47.74        18.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       20.81        22.92         1.18         8.55        13.02        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 
       10.59         0.66        17.10        14.76         1.51        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A69H 
       23.38         1.12        44.42        45.93         0.26        14.60 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 
       18.48        44.81         0.66         4.24         8.22         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT 
        3.19         3.39         4.24         3.35         7.20         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD 
        9.86         9.96        10.36        11.93        11.41         9.99 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II 
        8.94         7.13        21.34         9.83        12.00        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU 
       12.56         8.61         9.14         9.86         4.60        11.31 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        9.17         6.94         8.15        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.33       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       11.47        12.95        45.11        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       18.35        13.64        21.14        27.19        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        26.37        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       35.67       114.35        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       76.41        55.40        12.53        71.80        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU 
       42.81        61.68        13.64        14.20        59.31        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       50.33        46.82         5.59        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       40.54        40.83        13.97        40.47        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       37.64        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       29.52        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.21        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
       18.61        19.99         4.64        23.74        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       26.63        25.78        50.33        35.08        90.48        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       82.62        59.93        72.39        80.71        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       64.77        62.47        66.25        65.39        60.99        53.69 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       29.92        26.93        28.08        13.91        13.35         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20        12.82         0.20        14.04        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.35         1.84         0.20        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       19.59         0.62        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-G3-A25S 
       19.10        27.88        12.03         0.03         0.33        13.68 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       51.06        53.79        28.27        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
        5.92        19.53        19.23        25.25        22.95        24.46 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       20.42        17.10        14.70        20.78        11.87        14.14 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       15.78        15.65        11.80        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A9DB TCGA-HP-A5MZ 
       11.64         2.14        11.87        28.90         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 
       37.71        17.06        16.83        11.80        27.25        29.79 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       13.97        12.03         9.57        16.67        22.95        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        7.53        10.85        58.88        26.27        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB 
        3.09         0.72         0.49         0.30        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.04        15.39        15.52        36.10        27.88        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 
       16.44         1.71        15.98        10.75        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE 
       12.99        20.22        24.85        18.28        33.86        30.41 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       22.78        13.55        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        79.30        11.21 

  ZNF512B MUTATED ZNF512B WILD-TYPE 
             0.39              0.03 
  ZNF512B MUTATED ZNF512B WILD-TYPE 
            81.73            120.82 
  ZNF512B MUTATED ZNF512B WILD-TYPE 
            22.03             19.76 
[1] "0.4 - 81.7 (22.0)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.4"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ZNF512B MUTATED         4        2         0          2          0          0
  ZNF512B WILD-TYPE     170       84         3         62          9          9
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  ZNF512B MUTATED          0         0         0
  ZNF512B WILD-TYPE        2         1         2
D14V3, multiclass
            clus
vv           ZNF512B MUTATED ZNF512B WILD-TYPE
  STAGE I                  4               170
  STAGE II                 2                84
  STAGE III                0                 3
  STAGE IIIA               2                62
  STAGE IIIB               0                 9
  STAGE IIIC               0                 9
  STAGE IV                 0                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZNF512B MUTATED     4   2   2   0
  ZNF512B WILD-TYPE 180  92  77  13
D14V4, multiclass
    clus
vv   ZNF512B MUTATED ZNF512B WILD-TYPE
  T1               4               180
  T2               2                92
  T3               2                77
  T4               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V5, binary
                   cls
clus                  0   1
  ZNF512B MUTATED     4   0
  ZNF512B WILD-TYPE 250   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF512B MUTATED      4    0
  ZNF512B WILD-TYPE  250    4
   clus
vv  ZNF512B MUTATED ZNF512B WILD-TYPE
  0               4               250
  1               0                 4
[1] 2 2
[1] FALSE
D14V6, binary
                   cls
clus                  0   1
  ZNF512B MUTATED     6   0
  ZNF512B WILD-TYPE 263   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF512B MUTATED      6    0
  ZNF512B WILD-TYPE  263    4
   clus
vv  ZNF512B MUTATED ZNF512B WILD-TYPE
  0               6               263
  1               0                 4
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  ZNF512B MUTATED     5   3
  ZNF512B WILD-TYPE 116 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF512B MUTATED      5    3
  ZNF512B WILD-TYPE  116  249
        clus
vv       ZNF512B MUTATED ZNF512B WILD-TYPE
  FEMALE               5               116
  MALE                 3               249
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                  0   1
  ZNF512B MUTATED     7   0
  ZNF512B WILD-TYPE 334   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF512B MUTATED      7    0
  ZNF512B WILD-TYPE  334    9
     clus
vv    ZNF512B MUTATED ZNF512B WILD-TYPE
  NO                7               334
  YES               0                 9
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  ZNF512B MUTATED                         0                        8
  ZNF512B WILD-TYPE                       3                      355
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  ZNF512B MUTATED                                  0
  ZNF512B WILD-TYPE                                7
D14V9, multiclass
                                  clus
vv                                 ZNF512B MUTATED ZNF512B WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 3
  HEPATOCELLULAR CARCINOMA                       8               355
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZNF512B MUTATED     6   1   0   1
  ZNF512B WILD-TYPE 321  15   1  21
D14V10, multiclass
    clus
vv   ZNF512B MUTATED ZNF512B WILD-TYPE
  R0               6               321
  R1               1                15
  R2               0                 1
  RX               1                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF512B MUTATED                                  0     1
  ZNF512B WILD-TYPE                                2   159
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZNF512B MUTATED                           1     6
  ZNF512B WILD-TYPE                        16   178
D14V11, multiclass
                                  clus
vv                                 ZNF512B MUTATED ZNF512B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1               159
  BLACK OR AFRICAN AMERICAN                      1                16
  WHITE                                          6               178
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V12, binary
                   cls
clus                  0   1
  ZNF512B MUTATED     1   7
  ZNF512B WILD-TYPE  17 330
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF512B MUTATED      1    7
  ZNF512B WILD-TYPE   17  330
                        clus
vv                       ZNF512B MUTATED ZNF512B WILD-TYPE
  HISPANIC OR LATINO                   1                17
  NOT HISPANIC OR LATINO               7               330
[1] 2 2
[1] FALSE

Clustering(15) Variable = KCNN3 MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2               0   1
  KCNN3 MUTATED     7   5
  KCNN3 WILD-TYPE 230 125
  KCNN3 MUTATED KCNN3 WILD-TYPE 
             12             355 
  KCNN3 MUTATED KCNN3 WILD-TYPE 
              5             125 
$`KCNN3 MUTATED`
TCGA-BC-A112 TCGA-DD-AAEG TCGA-UB-A7MF TCGA-2Y-A9H1 TCGA-5R-AA1C TCGA-CC-A7IH 
        5.03        23.64         7.04        40.41        17.10        12.00 
TCGA-DD-AACI TCGA-DD-AADL TCGA-ED-A82E TCGA-ED-A8O6 TCGA-LG-A9QC TCGA-XR-A8TF 
       53.19        20.91        13.41         1.84        13.97        22.78 

$`KCNN3 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 
       21.83        18.90         9.96        22.62         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
       81.73        30.74        22.13        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-AA0V 
        2.14        31.27        12.72        24.56         0.76        10.32 
TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT 
       44.02        29.52         0.69        40.80        23.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       63.75        41.79        80.28        24.89        27.88       120.82 
TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       56.91        49.84        47.74        18.25        20.81        22.92 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
        1.18         8.55        13.02        10.78        10.59         0.66 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T 
       14.76         1.51        27.91        37.32        10.13        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 
       27.52         2.99        25.32        23.38         1.12        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 
       45.93         0.26        22.36        14.60        18.48        44.81 
TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 
       13.45         0.66         4.24         8.22         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 
        3.39         4.24         3.35         7.20         3.32         9.86 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE 
        9.96        10.36        11.93        11.41         9.99         8.94 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
        7.13        21.34         9.83        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
        9.14         9.86         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.15        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65        11.47        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       45.11        49.15         6.02        33.04        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       21.14        27.19        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF 
       13.78        30.61        33.14        32.52        21.70        30.97 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       26.37        30.15        30.51        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      114.35        13.48         0.53        11.41        75.65        76.41 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        71.80        12.00        15.42         6.41 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       69.11         0.30         3.52        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV 
       13.64        14.20        59.31        51.35        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       46.82         5.59        47.67         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        42.58        44.22        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.83        13.97        40.47        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.67        35.05        34.49         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        23.74        15.72        25.08        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        90.48        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.39        80.71        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        60.99        53.69        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       28.08        13.91        13.35         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-ED-A97K TCGA-EP-A12J 
        0.20        14.04        13.15        13.35         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       19.99        20.61        19.59         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       25.25        22.95        24.46        20.42        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       20.78        11.87        14.14        15.78        15.65        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       12.23        13.55         0.89        11.64         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75C 
       16.83        11.80        27.25        29.79        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       18.28        33.86        30.41        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.21        35.87        25.15        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  KCNN3 MUTATED KCNN3 WILD-TYPE 
           1.84            0.03 
  KCNN3 MUTATED KCNN3 WILD-TYPE 
          53.19          120.82 
  KCNN3 MUTATED KCNN3 WILD-TYPE 
         15.535          19.790 
[1] "1.8 - 53.2 (15.5)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.6"
D15V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  KCNN3 MUTATED         5        2         0          4          0          0
  KCNN3 WILD-TYPE     169       84         3         60          9          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  KCNN3 MUTATED          0         0         0
  KCNN3 WILD-TYPE        2         1         2
D15V3, multiclass
            clus
vv           KCNN3 MUTATED KCNN3 WILD-TYPE
  STAGE I                5             169
  STAGE II               2              84
  STAGE III              0               3
  STAGE IIIA             4              60
  STAGE IIIB             0               9
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCNN3 MUTATED     5   2   5   0
  KCNN3 WILD-TYPE 179  92  74  13
D15V4, multiclass
    clus
vv   KCNN3 MUTATED KCNN3 WILD-TYPE
  T1             5             179
  T2             2              92
  T3             5              74
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V5, binary
                 cls
clus                0   1
  KCNN3 MUTATED     7   0
  KCNN3 WILD-TYPE 247   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN3 MUTATED      7    0
  KCNN3 WILD-TYPE  247    4
   clus
vv  KCNN3 MUTATED KCNN3 WILD-TYPE
  0             7             247
  1             0               4
[1] 2 2
[1] FALSE
D15V6, binary
                 cls
clus                0   1
  KCNN3 MUTATED     8   0
  KCNN3 WILD-TYPE 261   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN3 MUTATED      8    0
  KCNN3 WILD-TYPE  261    4
   clus
vv  KCNN3 MUTATED KCNN3 WILD-TYPE
  0             8             261
  1             0               4
[1] 2 2
[1] FALSE
D15V7, binary
                 cls
clus                0   1
  KCNN3 MUTATED     3   9
  KCNN3 WILD-TYPE 118 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN3 MUTATED      3    9
  KCNN3 WILD-TYPE  118  243
        clus
vv       KCNN3 MUTATED KCNN3 WILD-TYPE
  FEMALE             3             118
  MALE               9             243
[1] 2 2
[1] FALSE
D15V8, binary
                 cls
clus                0   1
  KCNN3 MUTATED    12   0
  KCNN3 WILD-TYPE 329   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN3 MUTATED     12    0
  KCNN3 WILD-TYPE  329    9
     clus
vv    KCNN3 MUTATED KCNN3 WILD-TYPE
  NO             12             329
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  KCNN3 MUTATED                         0                       12
  KCNN3 WILD-TYPE                       3                      351
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  KCNN3 MUTATED                                  0
  KCNN3 WILD-TYPE                                7
D15V9, multiclass
                                  clus
vv                                 KCNN3 MUTATED KCNN3 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                    12             351
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KCNN3 MUTATED    12   0   0   0
  KCNN3 WILD-TYPE 315  16   1  22
D15V10, multiclass
    clus
vv   KCNN3 MUTATED KCNN3 WILD-TYPE
  R0            12             315
  R1             0              16
  R2             0               1
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KCNN3 MUTATED                                  0     6
  KCNN3 WILD-TYPE                                2   154
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KCNN3 MUTATED                           0     6
  KCNN3 WILD-TYPE                        17   178
D15V11, multiclass
                                  clus
vv                                 KCNN3 MUTATED KCNN3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        6             154
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        6             178
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V12, binary
                 cls
clus                0   1
  KCNN3 MUTATED     1  11
  KCNN3 WILD-TYPE  17 326
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN3 MUTATED      1   11
  KCNN3 WILD-TYPE   17  326
                        clus
vv                       KCNN3 MUTATED KCNN3 WILD-TYPE
  HISPANIC OR LATINO                 1              17
  NOT HISPANIC OR LATINO            11             326
[1] 2 2
[1] FALSE

Clustering(16) Variable = KRT10 MUTATION ANALYSIS
D16V1, survival
                 sevent
clus2               0   1
  KRT10 MUTATED     9   0
  KRT10 WILD-TYPE 228 130
  KRT10 MUTATED KRT10 WILD-TYPE 
              9             358 
  KRT10 MUTATED KRT10 WILD-TYPE 
              0             130 
$`KRT10 MUTATED`
TCGA-DD-AACK TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AAE0 TCGA-DD-AAEE TCGA-DD-AAVR 
        0.30        42.81        61.68        18.25        26.63        82.62 
TCGA-DD-AAW0 TCGA-ED-A97K TCGA-MI-A75C 
       66.25         0.20         9.57 

$`KRT10 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       21.34         9.83        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
        9.14         9.86         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.15        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65        11.47        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       45.11        49.15         6.02        33.04        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       21.14        27.19        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF 
       13.78        30.61        33.14        32.52        21.70        30.97 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       26.37        30.15        30.51        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      114.35        13.48         0.53        11.41        75.65        76.41 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        71.80        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
       53.19        69.11         3.52        58.16        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       34.49        20.91         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
       14.33        66.67        15.58        18.21        19.30        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 
       18.15        20.98        18.61        19.99         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       15.72        25.08        25.78        50.33        35.08        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       89.69        59.93        72.39        80.71        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       64.77        62.47        65.39        60.99        53.69        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       26.93        28.08        13.91        13.35         9.73         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
       12.82         0.20        14.04        13.15        13.41        13.35 
TCGA-ED-A8O6 TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        1.84        18.74        19.99        20.61        19.59         0.62 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       19.53        19.23        25.25        22.95        24.46        20.42 
TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       17.10        14.70        20.78        11.87        14.14        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.65        11.80        12.23        13.55         0.89        11.64 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 
       37.71        17.06        16.83        11.80        27.25        29.79 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       13.97        12.03        16.67        22.95        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        26.27        17.69        21.01         3.09 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        15.52        36.10        27.88        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        1.71        15.98        10.75        11.34         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       20.22        24.85        18.28        33.86        30.41        22.78 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       13.55        35.77        25.71        23.21        35.87        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        79.30        11.21 

  KRT10 MUTATED KRT10 WILD-TYPE 
           0.20            0.03 
  KRT10 MUTATED KRT10 WILD-TYPE 
          82.62          120.82 
  KRT10 MUTATED KRT10 WILD-TYPE 
          26.63           19.76 
[1] "0.2 - 82.6 (26.6)"  "0.0 - 120.8 (19.8)"
[1] "hr="     "2.6e+07"
D16V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  KRT10 MUTATED         7        0         0          2          0          0
  KRT10 WILD-TYPE     167       86         3         62          9          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  KRT10 MUTATED          0         0         0
  KRT10 WILD-TYPE        2         1         2
D16V3, multiclass
            clus
vv           KRT10 MUTATED KRT10 WILD-TYPE
  STAGE I                7             167
  STAGE II               0              86
  STAGE III              0               3
  STAGE IIIA             2              62
  STAGE IIIB             0               9
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KRT10 MUTATED     7   0   2   0
  KRT10 WILD-TYPE 177  94  77  13
D16V4, multiclass
    clus
vv   KRT10 MUTATED KRT10 WILD-TYPE
  T1             7             177
  T2             0              94
  T3             2              77
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V5, binary
                 cls
clus                0   1
  KRT10 MUTATED     9   0
  KRT10 WILD-TYPE 245   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT10 MUTATED      9    0
  KRT10 WILD-TYPE  245    4
   clus
vv  KRT10 MUTATED KRT10 WILD-TYPE
  0             9             245
  1             0               4
[1] 2 2
[1] FALSE
D16V6, binary
                 cls
clus                0   1
  KRT10 MUTATED     9   0
  KRT10 WILD-TYPE 260   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT10 MUTATED      9    0
  KRT10 WILD-TYPE  260    4
   clus
vv  KRT10 MUTATED KRT10 WILD-TYPE
  0             9             260
  1             0               4
[1] 2 2
[1] FALSE
D16V7, binary
                 cls
clus                0   1
  KRT10 MUTATED     1   8
  KRT10 WILD-TYPE 120 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT10 MUTATED      1    8
  KRT10 WILD-TYPE  120  244
        clus
vv       KRT10 MUTATED KRT10 WILD-TYPE
  FEMALE             1             120
  MALE               8             244
[1] 2 2
[1] FALSE
D16V8, binary
                 cls
clus                0   1
  KRT10 MUTATED     9   0
  KRT10 WILD-TYPE 332   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT10 MUTATED      9    0
  KRT10 WILD-TYPE  332    9
     clus
vv    KRT10 MUTATED KRT10 WILD-TYPE
  NO              9             332
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  KRT10 MUTATED                         0                        8
  KRT10 WILD-TYPE                       3                      355
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  KRT10 MUTATED                                  1
  KRT10 WILD-TYPE                                6
D16V9, multiclass
                                  clus
vv                                 KRT10 MUTATED KRT10 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                     8             355
  HEPATOCHOLANGIOCARCINOMA (MIXED)             1               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KRT10 MUTATED     9   0   0   0
  KRT10 WILD-TYPE 318  16   1  22
D16V10, multiclass
    clus
vv   KRT10 MUTATED KRT10 WILD-TYPE
  R0             9             318
  R1             0              16
  R2             0               1
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRT10 MUTATED                                  0     8
  KRT10 WILD-TYPE                                2   152
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KRT10 MUTATED                           0     1
  KRT10 WILD-TYPE                        17   183
D16V11, multiclass
                                  clus
vv                                 KRT10 MUTATED KRT10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        8             152
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        1             183
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V12, binary
                 cls
clus                0   1
  KRT10 MUTATED     0   9
  KRT10 WILD-TYPE  18 328
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT10 MUTATED      0    9
  KRT10 WILD-TYPE   18  328
                        clus
vv                       KRT10 MUTATED KRT10 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             9             328
[1] 2 2
[1] FALSE

Clustering(17) Variable = APOB MUTATION ANALYSIS
D17V1, survival
                sevent
clus2              0   1
  APOB MUTATED    21  18
  APOB WILD-TYPE 216 112
  APOB MUTATED APOB WILD-TYPE 
            39            328 
  APOB MUTATED APOB WILD-TYPE 
            18            112 
$`APOB MUTATED`
TCGA-4R-AA8I TCGA-G3-A25W TCGA-KR-A7K0 TCGA-BC-A10Z TCGA-CC-A3MA TCGA-CC-A7IG 
        8.61        30.74         2.14         1.12         9.96         9.83 
TCGA-CC-A7IH TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A1EK TCGA-DD-A3A0 TCGA-DD-A3A5 
       12.00        79.40        11.47        18.35        25.81       102.74 
TCGA-DD-A3A7 TCGA-DD-A4NG TCGA-DD-A4NS TCGA-DD-AACB TCGA-DD-AACG TCGA-DD-AAD2 
       13.78        26.37        80.75        76.41        15.42        21.63 
TCGA-DD-AAD5 TCGA-DD-AADG TCGA-DD-AAE9 TCGA-DD-AAEE TCGA-DD-AAEI TCGA-ED-A7XP 
       44.22        37.64        23.74        26.63        50.33        13.15 
TCGA-EP-A12J TCGA-FV-A2QQ TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A7M6 TCGA-G3-A7M8 
       18.74        23.97         5.92        19.53        20.78        14.14 
TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-HP-A5MZ TCGA-LG-A9QD TCGA-RC-A6M4 TCGA-RC-A7S9 
        0.89         2.14         2.99        12.03         0.72        21.04 
TCGA-UB-A7MB TCGA-YA-A8S7 TCGA-ZS-A9CD 
       19.76        13.55        45.57 

$`APOB WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        11.74        38.40        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
        6.38        81.73        22.13        22.06         1.84        20.75 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V 
       31.27        12.72        24.56         0.76         7.04        10.32 
TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT 
       44.02        29.52         0.69        40.80        23.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       63.75        41.79        80.28        24.89        27.88       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 
       40.41        56.91        49.84        47.74        18.25        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH 
       22.92         1.18         8.55        13.02        10.78        10.59 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q 
        0.66        17.10        14.76         1.51        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       10.13        27.52        27.52         2.99        25.32        23.38 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO 
       44.42        45.93         0.26        22.36        14.60        18.48 
TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 
       44.81        13.45         0.66         4.24         8.22         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT 
        3.19         3.39         4.24         3.35         7.20         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE 
        9.86        10.36        11.93        11.41         9.99         8.94 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        7.13        21.34        13.12        12.56         8.61         9.14 
TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.86         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EB 
        2.60         0.46        21.76        51.29        90.71        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       33.04        13.64        21.14        27.19        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 
       19.76         7.66        70.06        17.59        20.12       107.11 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NH 
       30.61        33.14        32.52        21.70        30.97        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       12.26         0.30        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       11.41        75.65        55.40        12.53        71.80        12.00 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       42.81        61.68        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
        4.50        18.54        42.58        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADI 
       40.83        13.97        40.47        39.52         3.78        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.05        34.49        20.91         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP 
        4.64        15.72        25.08        25.78        35.08        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       89.69        82.62        59.93        72.39        80.71        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        60.99 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A82E 
        9.73         0.20        12.82         0.20        14.04        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       13.35         1.84         0.20        19.99        20.61        19.59 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 
        0.62        11.93        14.40        60.89        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CK 
       53.79        28.27        14.86        21.53        25.64        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       25.25        22.95        24.46        20.42        17.10        14.70 
TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       11.87        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV5 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 
       11.64        11.87        28.90         1.02         2.20        37.71 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06        16.83        11.80        27.25        29.79        13.97 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M5 
       58.88        26.27        17.69        21.01         3.09         0.49 
TCGA-RC-A6M6 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
        0.30        19.33        19.04        15.39        15.52        36.10 
TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L 
       27.88        16.44         1.71        15.98        10.75        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD 
        0.99        12.99        20.22        24.85        18.28        33.86 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       30.41        22.78        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        79.30        11.21 

  APOB MUTATED APOB WILD-TYPE 
          0.72           0.03 
  APOB MUTATED APOB WILD-TYPE 
        102.74         120.82 
  APOB MUTATED APOB WILD-TYPE 
         18.74          19.99 
[1] "0.7 - 102.7 (18.7)" "0.0 - 120.8 (20.0)"
[1] "hr=" "1.5"
D17V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  APOB MUTATED        18        8         1          9          2          0
  APOB WILD-TYPE     156       78         2         55          7          9
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  APOB MUTATED          0         0         1
  APOB WILD-TYPE        2         1         1
D17V3, multiclass
            clus
vv           APOB MUTATED APOB WILD-TYPE
  STAGE I              18            156
  STAGE II              8             78
  STAGE III             1              2
  STAGE IIIA            9             55
  STAGE IIIB            2              7
  STAGE IIIC            0              9
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             1              1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  APOB MUTATED    18   8  12   1
  APOB WILD-TYPE 166  86  67  12
D17V4, multiclass
    clus
vv   APOB MUTATED APOB WILD-TYPE
  T1           18            166
  T2            8             86
  T3           12             67
  T4            1             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V5, binary
                cls
clus               0   1
  APOB MUTATED    29   0
  APOB WILD-TYPE 225   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED     29    0
  APOB WILD-TYPE  225    4
   clus
vv  APOB MUTATED APOB WILD-TYPE
  0           29            225
  1            0              4
[1] 2 2
[1] FALSE
D17V6, binary
                cls
clus               0   1
  APOB MUTATED    28   1
  APOB WILD-TYPE 241   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED     28    1
  APOB WILD-TYPE  241    3
   clus
vv  APOB MUTATED APOB WILD-TYPE
  0           28            241
  1            1              3
[1] 2 2
[1] FALSE
D17V7, binary
                cls
clus               0   1
  APOB MUTATED    12  27
  APOB WILD-TYPE 109 225
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED     12   27
  APOB WILD-TYPE  109  225
        clus
vv       APOB MUTATED APOB WILD-TYPE
  FEMALE           12            109
  MALE             27            225
[1] 2 2
[1] FALSE
D17V8, binary
                cls
clus               0   1
  APOB MUTATED    37   0
  APOB WILD-TYPE 304   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED     37    0
  APOB WILD-TYPE  304    9
     clus
vv    APOB MUTATED APOB WILD-TYPE
  NO            37            304
  YES            0              9
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  APOB MUTATED                         0                       39
  APOB WILD-TYPE                       3                      324
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  APOB MUTATED                                  0
  APOB WILD-TYPE                                7
D17V9, multiclass
                                  clus
vv                                 APOB MUTATED APOB WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              3
  HEPATOCELLULAR CARCINOMA                   39            324
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  APOB MUTATED    37   1   0   1
  APOB WILD-TYPE 290  15   1  21
D17V10, multiclass
    clus
vv   APOB MUTATED APOB WILD-TYPE
  R0           37            290
  R1            1             15
  R2            0              1
  RX            1             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  APOB MUTATED                                  1    15
  APOB WILD-TYPE                                1   145
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  APOB MUTATED                           1    20
  APOB WILD-TYPE                        16   164
D17V11, multiclass
                                  clus
vv                                 APOB MUTATED APOB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              1
  ASIAN                                      15            145
  BLACK OR AFRICAN AMERICAN                   1             16
  WHITE                                      20            164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V12, binary
                cls
clus               0   1
  APOB MUTATED     2  34
  APOB WILD-TYPE  16 303
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED      2   34
  APOB WILD-TYPE   16  303
                        clus
vv                       APOB MUTATED APOB WILD-TYPE
  HISPANIC OR LATINO                2             16
  NOT HISPANIC OR LATINO           34            303
[1] 2 2
[1] FALSE

Clustering(18) Variable = MLL4 MUTATION ANALYSIS
D18V1, survival
                sevent
clus2              0   1
  MLL4 MUTATED     9  10
  MLL4 WILD-TYPE 228 120
  MLL4 MUTATED MLL4 WILD-TYPE 
            19            348 
  MLL4 MUTATED MLL4 WILD-TYPE 
            10            120 
$`MLL4 MUTATED`
TCGA-4R-AA8I TCGA-G3-A3CG TCGA-5R-AAAM TCGA-CC-5258 TCGA-CC-A7II TCGA-DD-A119 
        8.61        22.13         1.51         4.24        13.12         7.33 
TCGA-DD-A11B TCGA-DD-A1EG TCGA-DD-A39Y TCGA-DD-A73E TCGA-DD-AAD0 TCGA-DD-AADG 
        0.46        45.11         5.62         1.45         4.50        37.64 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-ED-A7PZ TCGA-EP-A2KA TCGA-FV-A2QR TCGA-G3-A3CJ 
       15.72        25.08         0.20        20.61        19.10        19.53 
TCGA-HP-A5MZ 
        2.99 

$`MLL4 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        11.74        38.40        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
        6.38        81.73        30.74        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
        2.14        31.27        12.72        24.56         0.76         7.04 
TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
       10.32        44.02        29.52         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
      120.82        40.41        56.91        49.84        47.74        18.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       20.81        22.92         1.18         8.55        13.02        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-BC-4073 TCGA-BC-A10Q 
       10.59         0.66        17.10        14.76        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       10.13        27.52        27.52         2.99        25.32        23.38 
TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        1.12        44.42        45.93         0.26        22.36        14.60 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5259 TCGA-CC-5260 
       18.48        44.81        13.45         0.66         8.22         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT 
        3.19         3.39         4.24         3.35         7.20         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD 
        9.86         9.96        10.36        11.93        11.41         9.99 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7IJ 
        8.94         7.13        21.34         9.83        12.00        12.56 
TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
        8.61         9.14         9.86         4.60        11.31         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        6.94         8.15        79.73        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
      113.00         2.60        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH 
       66.31        19.79        75.65        11.47        12.95        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.69        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ 
       32.52        21.70        30.97        26.37        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
       22.78        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        5.62        18.54        21.63        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
        3.78        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       29.52        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.21        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEE TCGA-DD-AAEH 
       18.61        19.99         4.64        23.74        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        90.48        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.39        80.71        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        60.99        53.69        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       28.08        13.91        13.35         9.73         0.20        12.82 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        19.99        19.59         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       60.89        23.97        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.39        13.68        51.06        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       21.53        25.64         5.92        19.23        25.25        22.95 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       24.46        20.42        17.10        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        0.89        11.64         2.14        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 
        2.20        37.71        17.06        16.83        11.80        27.25 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       29.79        13.97        12.03         9.57        16.67        22.95 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         7.53        10.85        58.88        26.27        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 
       21.01         3.09         0.72         0.49         0.30        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       19.33        19.04        15.39        15.52        36.10        27.88 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L 
       19.76        16.44         1.71        15.98        10.75        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD 
        0.99        12.99        20.22        24.85        18.28        33.86 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       30.41        22.78        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.87        25.15        12.99        45.57        79.30        11.21 

  MLL4 MUTATED MLL4 WILD-TYPE 
          0.20           0.03 
  MLL4 MUTATED MLL4 WILD-TYPE 
         45.11         120.82 
  MLL4 MUTATED MLL4 WILD-TYPE 
          8.61          20.17 
[1] "0.2 - 45.1 (8.6)"   "0.0 - 120.8 (20.2)"
[1] "hr=" "3"  
D18V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  MLL4 MUTATED        10        5         0          3          0          0
  MLL4 WILD-TYPE     164       81         3         61          9          9
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  MLL4 MUTATED          1         0         0
  MLL4 WILD-TYPE        1         1         2
D18V3, multiclass
            clus
vv           MLL4 MUTATED MLL4 WILD-TYPE
  STAGE I              10            164
  STAGE II              5             81
  STAGE III             0              3
  STAGE IIIA            3             61
  STAGE IIIB            0              9
  STAGE IIIC            0              9
  STAGE IV              1              1
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MLL4 MUTATED    10   5   4   0
  MLL4 WILD-TYPE 174  89  75  13
D18V4, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  T1           10            174
  T2            5             89
  T3            4             75
  T4            0             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V5, binary
                cls
clus               0   1
  MLL4 MUTATED    14   0
  MLL4 WILD-TYPE 240   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     14    0
  MLL4 WILD-TYPE  240    4
   clus
vv  MLL4 MUTATED MLL4 WILD-TYPE
  0           14            240
  1            0              4
[1] 2 2
[1] FALSE
D18V6, binary
                cls
clus               0   1
  MLL4 MUTATED    16   1
  MLL4 WILD-TYPE 253   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     16    1
  MLL4 WILD-TYPE  253    3
   clus
vv  MLL4 MUTATED MLL4 WILD-TYPE
  0           16            253
  1            1              3
[1] 2 2
[1] FALSE
D18V7, binary
                cls
clus               0   1
  MLL4 MUTATED     3  16
  MLL4 WILD-TYPE 118 236
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED      3   16
  MLL4 WILD-TYPE  118  236
        clus
vv       MLL4 MUTATED MLL4 WILD-TYPE
  FEMALE            3            118
  MALE             16            236
[1] 2 2
[1] FALSE
D18V8, binary
                cls
clus               0   1
  MLL4 MUTATED    18   0
  MLL4 WILD-TYPE 323   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     18    0
  MLL4 WILD-TYPE  323    9
     clus
vv    MLL4 MUTATED MLL4 WILD-TYPE
  NO            18            323
  YES            0              9
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  MLL4 MUTATED                         0                       19
  MLL4 WILD-TYPE                       3                      344
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  MLL4 MUTATED                                  0
  MLL4 WILD-TYPE                                7
D18V9, multiclass
                                  clus
vv                                 MLL4 MUTATED MLL4 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              3
  HEPATOCELLULAR CARCINOMA                   19            344
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MLL4 MUTATED    14   1   1   3
  MLL4 WILD-TYPE 313  15   0  19
D18V10, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  R0           14            313
  R1            1             15
  R2            1              0
  RX            3             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLL4 MUTATED                                  1     9
  MLL4 WILD-TYPE                                1   151
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MLL4 MUTATED                           0     8
  MLL4 WILD-TYPE                        17   176
D18V11, multiclass
                                  clus
vv                                 MLL4 MUTATED MLL4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              1
  ASIAN                                       9            151
  BLACK OR AFRICAN AMERICAN                   0             17
  WHITE                                       8            176
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V12, binary
                cls
clus               0   1
  MLL4 MUTATED     0  18
  MLL4 WILD-TYPE  18 319
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED      0   18
  MLL4 WILD-TYPE   18  319
                        clus
vv                       MLL4 MUTATED MLL4 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO           18            319
[1] 2 2
[1] FALSE

Clustering(19) Variable = ALB MUTATION ANALYSIS
D19V1, survival
               sevent
clus2             0   1
  ALB MUTATED    30  12
  ALB WILD-TYPE 207 118
  ALB MUTATED ALB WILD-TYPE 
           42           325 
  ALB MUTATED ALB WILD-TYPE 
           12           118 
$`ALB MUTATED`
TCGA-DD-A4NI TCGA-DD-AAE8 TCGA-EP-A3JL TCGA-ES-A2HS TCGA-2Y-A9GS TCGA-2Y-A9GZ 
       26.83        21.83         9.96        22.62        23.80        27.88 
TCGA-3K-AAZ8 TCGA-BC-A8YO TCGA-CC-A5UE TCGA-CC-A8HT TCGA-DD-A118 TCGA-DD-A1E9 
       13.02        18.48         8.94         4.60       113.00        90.71 
TCGA-DD-A1EE TCGA-DD-A39X TCGA-DD-A4NK TCGA-DD-AACH TCGA-DD-AACK TCGA-DD-AACN 
       11.47        55.69        39.78         6.41         0.30        42.81 
TCGA-DD-AACO TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADG TCGA-DD-AADQ TCGA-DD-AADU 
       61.68        22.09        40.54        37.64        14.33        18.21 
TCGA-DD-AAVU TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-EP-A26S TCGA-FV-A2QQ TCGA-FV-A496 
       72.39        66.25        60.99        19.99        23.97         0.33 
TCGA-G3-A25S TCGA-G3-A3CJ TCGA-G3-AAV0 TCGA-G3-AAV5 TCGA-K7-A6G5 TCGA-K7-AAU7 
       13.68        19.53        15.65        11.64        16.83        11.80 
TCGA-LG-A9QD TCGA-MI-A75G TCGA-WQ-AB4B TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.03        22.95        12.99        45.57        79.30        11.21 

$`ALB WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-AADV TCGA-DD-AAE7 
       17.98        36.66         0.36        90.28        18.87        21.17 
TCGA-DD-AAEA TCGA-DD-AAEG TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W 
       18.90        23.64         8.12         6.38        81.73        30.74 
TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 
       22.13        22.06         1.84        20.75         2.14        31.27 
TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC 
       12.72        24.56         0.76         7.04        10.32        44.02 
TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW 
       29.52         0.69        40.80        53.39        63.75        41.79 
TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       80.28        24.89       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        17.10        14.76         1.51 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       22.36        14.60        44.81        13.45         0.66         4.24 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
        8.22         2.86         3.19         3.39         4.24         3.35 
TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        7.20         3.32         9.86         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
       11.41         9.99         7.13        21.34         9.83        12.00 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HU 
       13.12        12.56         8.61         9.14         9.86        11.31 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        9.17         6.94         8.15        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.33         7.33         2.60         0.46        21.76        51.29 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG 
       79.40        66.31        19.79        75.65        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       27.19         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       33.14        32.52        21.70        30.97        26.37        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       30.51        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM 
       12.00        15.42        53.19        69.11         3.52        58.16 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV 
       13.64        14.20        59.31        51.35        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       46.82         5.59        47.67         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC 
       21.63        42.58        44.22        40.08        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       40.47        39.52         3.78        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR 
       20.91         0.39        29.52        14.89        15.06        66.67 
TCGA-DD-AADS TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       15.58        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
       18.61        19.99         4.64        23.74        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       26.63        25.78        50.33        35.08        90.48        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       82.62        59.93        80.71        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW1 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       62.47        65.39        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        20.61        19.59         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A4ZQ 
       60.89        19.10        27.88        12.03         0.03         0.39 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       51.06        53.79        28.27        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
        5.92        19.23        25.25        22.95        24.46        20.42 
TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       17.10        14.70        20.78        11.87        14.14        15.78 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 
       11.80        12.23        13.55         0.89         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I 
       27.25        29.79        13.97         9.57        16.67        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        7.53        10.85        58.88        26.27        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB 
        3.09         0.72         0.49         0.30        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.04        15.39        15.52        36.10        27.88        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 
       16.44         1.71        15.98        10.75        11.34         0.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       20.22        24.85        18.28        33.86        30.41        22.78 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       13.55        35.77        25.71        23.21        35.87        25.15 
TCGA-ZP-A9D4 
       12.99 

  ALB MUTATED ALB WILD-TYPE 
         0.30          0.03 
  ALB MUTATED ALB WILD-TYPE 
       113.00        120.82 
  ALB MUTATED ALB WILD-TYPE 
        20.91         19.76 
[1] "0.3 - 113.0 (20.9)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1.4"
D19V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ALB MUTATED        17       16         0          6          2          1
  ALB WILD-TYPE     157       70         3         58          7          8
               vv
clus            STAGE IV STAGE IVA STAGE IVB
  ALB MUTATED          0         0         0
  ALB WILD-TYPE        2         1         2
D19V3, multiclass
            clus
vv           ALB MUTATED ALB WILD-TYPE
  STAGE I             17           157
  STAGE II            16            70
  STAGE III            0             3
  STAGE IIIA           6            58
  STAGE IIIB           2             7
  STAGE IIIC           1             8
  STAGE IV             0             2
  STAGE IVA            0             1
  STAGE IVB            0             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  ALB MUTATED    17  17   7   2
  ALB WILD-TYPE 167  77  72  11
D19V4, multiclass
    clus
vv   ALB MUTATED ALB WILD-TYPE
  T1          17           167
  T2          17            77
  T3           7            72
  T4           2            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V5, binary
               cls
clus              0   1
  ALB MUTATED    29   0
  ALB WILD-TYPE 225   4
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALB MUTATED     29    0
  ALB WILD-TYPE  225    4
   clus
vv  ALB MUTATED ALB WILD-TYPE
  0          29           225
  1           0             4
[1] 2 2
[1] FALSE
D19V6, binary
               cls
clus              0   1
  ALB MUTATED    30   0
  ALB WILD-TYPE 239   4
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALB MUTATED     30    0
  ALB WILD-TYPE  239    4
   clus
vv  ALB MUTATED ALB WILD-TYPE
  0          30           239
  1           0             4
[1] 2 2
[1] FALSE
D19V7, binary
               cls
clus              0   1
  ALB MUTATED     7  36
  ALB WILD-TYPE 114 216
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALB MUTATED      7   36
  ALB WILD-TYPE  114  216
        clus
vv       ALB MUTATED ALB WILD-TYPE
  FEMALE           7           114
  MALE            36           216
[1] 2 2
[1] FALSE
D19V8, binary
               cls
clus              0   1
  ALB MUTATED    40   1
  ALB WILD-TYPE 301   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALB MUTATED     40    1
  ALB WILD-TYPE  301    8
     clus
vv    ALB MUTATED ALB WILD-TYPE
  NO           40           301
  YES           1             8
[1] 2 2
[1] FALSE
               vv
clus            FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  ALB MUTATED                         0                       42
  ALB WILD-TYPE                       3                      321
               vv
clus            HEPATOCHOLANGIOCARCINOMA (MIXED)
  ALB MUTATED                                  1
  ALB WILD-TYPE                                6
D19V9, multiclass
                                  clus
vv                                 ALB MUTATED ALB WILD-TYPE
  FIBROLAMELLAR CARCINOMA                    0             3
  HEPATOCELLULAR CARCINOMA                  42           321
  HEPATOCHOLANGIOCARCINOMA (MIXED)           1             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  ALB MUTATED    37   1   0   3
  ALB WILD-TYPE 290  15   1  19
D19V10, multiclass
    clus
vv   ALB MUTATED ALB WILD-TYPE
  R0          37           290
  R1           1            15
  R2           0             1
  RX           3            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALB MUTATED                                  1    17
  ALB WILD-TYPE                                1   143
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ALB MUTATED                           1    24
  ALB WILD-TYPE                        16   160
D19V11, multiclass
                                  clus
vv                                 ALB MUTATED ALB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           1             1
  ASIAN                                     17           143
  BLACK OR AFRICAN AMERICAN                  1            16
  WHITE                                     24           160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V12, binary
               cls
clus              0   1
  ALB MUTATED     2  41
  ALB WILD-TYPE  16 296
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALB MUTATED      2   41
  ALB WILD-TYPE   16  296
                        clus
vv                       ALB MUTATED ALB WILD-TYPE
  HISPANIC OR LATINO               2            16
  NOT HISPANIC OR LATINO          41           296
[1] 2 2
[1] FALSE

Clustering(20) Variable = TSC2 MUTATION ANALYSIS
D20V1, survival
                sevent
clus2              0   1
  TSC2 MUTATED     5   7
  TSC2 WILD-TYPE 232 123
  TSC2 MUTATED TSC2 WILD-TYPE 
            12            355 
  TSC2 MUTATED TSC2 WILD-TYPE 
             7            123 
$`TSC2 MUTATED`
TCGA-CC-A7IJ TCGA-CC-A8HT TCGA-CC-A9FS TCGA-DD-A114 TCGA-DD-A1EE TCGA-DD-A39Z 
       12.56         4.60         6.94        37.78        11.47        19.76 
TCGA-DD-A3A1 TCGA-DD-A4NH TCGA-DD-A4NQ TCGA-DD-AACL TCGA-G3-AAV7 TCGA-MI-A75I 
        7.66        30.15        12.26         3.52        11.87        20.71 

$`TSC2 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A7IL 
       21.34         9.83        12.00        13.12         8.61         9.14 
TCGA-CC-A8HS TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A115 
        9.86        11.31         9.17         8.15        79.73        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.33       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        33.04        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 
       13.64        21.14        27.19        55.69         5.62        25.81 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       30.61        33.14        32.52        21.70        30.97        26.37 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        40.08        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        29.52        14.89        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       66.67        15.58        18.21        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 
       18.15        20.98        18.61        19.99         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       15.72        25.08        26.63        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       90.48        89.69        82.62        59.93        72.39        80.71 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       60.99        53.69        29.92        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         9.73         0.20        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       13.15        13.41        13.35         1.84         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       19.99        20.61        19.59         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       25.25        22.95        24.46        20.42        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       20.78        11.87        14.14        15.78        15.65        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-GJ-A3OU 
       12.23        13.55         0.89        11.64         2.14        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       16.67        22.95         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       17.69        21.01         3.09         0.72         0.49         0.30 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.04        19.33        19.04        15.39        15.52        36.10 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       27.88        19.76        16.44         1.71        15.98        10.75 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       11.34         0.99        12.99        20.22        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        22.78        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.21        35.87        25.15        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  TSC2 MUTATED TSC2 WILD-TYPE 
          3.52           0.03 
  TSC2 MUTATED TSC2 WILD-TYPE 
         37.78         120.82 
  TSC2 MUTATED TSC2 WILD-TYPE 
        12.065         19.990 
[1] "3.5 - 37.8 (12.1)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "2.8"
D20V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TSC2 MUTATED         1        6         0          3          1          0
  TSC2 WILD-TYPE     173       80         3         61          8          9
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  TSC2 MUTATED          0         0         0
  TSC2 WILD-TYPE        2         1         2
D20V3, multiclass
            clus
vv           TSC2 MUTATED TSC2 WILD-TYPE
  STAGE I               1            173
  STAGE II              6             80
  STAGE III             0              3
  STAGE IIIA            3             61
  STAGE IIIB            1              8
  STAGE IIIC            0              9
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TSC2 MUTATED     1   7   4   0
  TSC2 WILD-TYPE 183  87  75  13
D20V4, multiclass
    clus
vv   TSC2 MUTATED TSC2 WILD-TYPE
  T1            1            183
  T2            7             87
  T3            4             75
  T4            0             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V5, binary
                cls
clus               0   1
  TSC2 MUTATED     9   0
  TSC2 WILD-TYPE 245   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC2 MUTATED      9    0
  TSC2 WILD-TYPE  245    4
   clus
vv  TSC2 MUTATED TSC2 WILD-TYPE
  0            9            245
  1            0              4
[1] 2 2
[1] FALSE
D20V6, binary
                cls
clus               0   1
  TSC2 MUTATED    11   0
  TSC2 WILD-TYPE 258   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC2 MUTATED     11    0
  TSC2 WILD-TYPE  258    4
   clus
vv  TSC2 MUTATED TSC2 WILD-TYPE
  0           11            258
  1            0              4
[1] 2 2
[1] FALSE
D20V7, binary
                cls
clus               0   1
  TSC2 MUTATED     3   9
  TSC2 WILD-TYPE 118 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC2 MUTATED      3    9
  TSC2 WILD-TYPE  118  243
        clus
vv       TSC2 MUTATED TSC2 WILD-TYPE
  FEMALE            3            118
  MALE              9            243
[1] 2 2
[1] FALSE
D20V8, binary
                cls
clus               0   1
  TSC2 MUTATED    11   0
  TSC2 WILD-TYPE 330   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC2 MUTATED     11    0
  TSC2 WILD-TYPE  330    9
     clus
vv    TSC2 MUTATED TSC2 WILD-TYPE
  NO            11            330
  YES            0              9
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  TSC2 MUTATED                         0                       12
  TSC2 WILD-TYPE                       3                      351
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  TSC2 MUTATED                                  0
  TSC2 WILD-TYPE                                7
D20V9, multiclass
                                  clus
vv                                 TSC2 MUTATED TSC2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              3
  HEPATOCELLULAR CARCINOMA                   12            351
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TSC2 MUTATED    12   0   0   0
  TSC2 WILD-TYPE 315  16   1  22
D20V10, multiclass
    clus
vv   TSC2 MUTATED TSC2 WILD-TYPE
  R0           12            315
  R1            0             16
  R2            0              1
  RX            0             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TSC2 MUTATED                                  0     5
  TSC2 WILD-TYPE                                2   155
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TSC2 MUTATED                           2     3
  TSC2 WILD-TYPE                        15   181
D20V11, multiclass
                                  clus
vv                                 TSC2 MUTATED TSC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       5            155
  BLACK OR AFRICAN AMERICAN                   2             15
  WHITE                                       3            181
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V12, binary
                cls
clus               0   1
  TSC2 MUTATED     1   9
  TSC2 WILD-TYPE  17 328
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC2 MUTATED      1    9
  TSC2 WILD-TYPE   17  328
                        clus
vv                       TSC2 MUTATED TSC2 WILD-TYPE
  HISPANIC OR LATINO                1             17
  NOT HISPANIC OR LATINO            9            328
[1] 2 2
[1] FALSE

Clustering(21) Variable = IL6ST MUTATION ANALYSIS
D21V1, survival
                 sevent
clus2               0   1
  IL6ST MUTATED     9   3
  IL6ST WILD-TYPE 228 127
  IL6ST MUTATED IL6ST WILD-TYPE 
             12             355 
  IL6ST MUTATED IL6ST WILD-TYPE 
              3             127 
$`IL6ST MUTATED`
TCGA-ES-A2HS TCGA-CC-A123 TCGA-DD-A118 TCGA-DD-A1ED TCGA-DD-A4NL TCGA-DD-A4NP 
       22.62         7.20       113.00        75.65        56.25       108.76 
TCGA-DD-AADE TCGA-DD-AADQ TCGA-ED-A459 TCGA-ES-A2HT TCGA-G3-A3CK TCGA-WX-AA47 
       39.52        14.33        29.92        14.40        19.23        18.28 

$`IL6ST WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 
       21.17        21.83        18.90        23.64         9.96         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        20.81        22.92         1.18         8.55        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        17.10        14.76         1.51 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        14.60        18.48        44.81        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.24         8.22         2.86         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        3.35         3.32         9.86         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS 
       12.00        13.12        12.56         8.61         9.14         9.86 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       37.78        83.57        53.33         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       11.47        12.95        45.11        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       18.35        13.64        21.14        27.19        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       21.70        30.97        26.37        30.15        30.51        39.78 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56        73.81        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      114.35        13.48         0.53        11.41        75.65        76.41 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        71.80        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
       53.19        69.11         0.30         3.52        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
       61.68        13.64        14.20        59.31        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       50.33        46.82         5.59        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADG 
       40.54        40.83        13.97        40.47         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       35.67        35.05        34.49        20.91         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       14.89        15.06        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        23.74        15.72        25.08        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        90.48        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.39        80.71        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A4XI TCGA-ED-A5KG 
       66.25        65.39        60.99        53.69        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        20.61        19.59         0.62        11.93 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SI 
       14.86        21.53        25.64         5.92        19.53        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
       22.95        24.46        20.42        17.10        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       11.87        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        11.34         0.99        12.99        20.22        24.85 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        22.78        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.21        35.87        25.15        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  IL6ST MUTATED IL6ST WILD-TYPE 
           7.20            0.03 
  IL6ST MUTATED IL6ST WILD-TYPE 
         113.00          120.82 
  IL6ST MUTATED IL6ST WILD-TYPE 
          26.27           19.76 
[1] "7.2 - 113.0 (26.3)" "0.0 - 120.8 (19.8)"
[1] "hr=" "2.5"
D21V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  IL6ST MUTATED         7        3         0          2          0          0
  IL6ST WILD-TYPE     167       83         3         62          9          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  IL6ST MUTATED          0         0         0
  IL6ST WILD-TYPE        2         1         2
D21V3, multiclass
            clus
vv           IL6ST MUTATED IL6ST WILD-TYPE
  STAGE I                7             167
  STAGE II               3              83
  STAGE III              0               3
  STAGE IIIA             2              62
  STAGE IIIB             0               9
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IL6ST MUTATED     7   3   2   0
  IL6ST WILD-TYPE 177  91  77  13
D21V4, multiclass
    clus
vv   IL6ST MUTATED IL6ST WILD-TYPE
  T1             7             177
  T2             3              91
  T3             2              77
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V5, binary
                 cls
clus                0   1
  IL6ST MUTATED     9   0
  IL6ST WILD-TYPE 245   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL6ST MUTATED      9    0
  IL6ST WILD-TYPE  245    4
   clus
vv  IL6ST MUTATED IL6ST WILD-TYPE
  0             9             245
  1             0               4
[1] 2 2
[1] FALSE
D21V6, binary
                 cls
clus                0   1
  IL6ST MUTATED     9   0
  IL6ST WILD-TYPE 260   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL6ST MUTATED      9    0
  IL6ST WILD-TYPE  260    4
   clus
vv  IL6ST MUTATED IL6ST WILD-TYPE
  0             9             260
  1             0               4
[1] 2 2
[1] FALSE
D21V7, binary
                 cls
clus                0   1
  IL6ST MUTATED     3   9
  IL6ST WILD-TYPE 118 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL6ST MUTATED      3    9
  IL6ST WILD-TYPE  118  243
        clus
vv       IL6ST MUTATED IL6ST WILD-TYPE
  FEMALE             3             118
  MALE               9             243
[1] 2 2
[1] FALSE
D21V8, binary
                 cls
clus                0   1
  IL6ST MUTATED     8   2
  IL6ST WILD-TYPE 333   7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL6ST MUTATED      8    2
  IL6ST WILD-TYPE  333    7
     clus
vv    IL6ST MUTATED IL6ST WILD-TYPE
  NO              8             333
  YES             2               7
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  IL6ST MUTATED                         0                       12
  IL6ST WILD-TYPE                       3                      351
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  IL6ST MUTATED                                  0
  IL6ST WILD-TYPE                                7
D21V9, multiclass
                                  clus
vv                                 IL6ST MUTATED IL6ST WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                    12             351
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  IL6ST MUTATED    11   0   0   1
  IL6ST WILD-TYPE 316  16   1  21
D21V10, multiclass
    clus
vv   IL6ST MUTATED IL6ST WILD-TYPE
  R0            11             316
  R1             0              16
  R2             0               1
  RX             1              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL6ST MUTATED                                  0     5
  IL6ST WILD-TYPE                                2   155
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IL6ST MUTATED                           1     6
  IL6ST WILD-TYPE                        16   178
D21V11, multiclass
                                  clus
vv                                 IL6ST MUTATED IL6ST WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        5             155
  BLACK OR AFRICAN AMERICAN                    1              16
  WHITE                                        6             178
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V12, binary
                 cls
clus                0   1
  IL6ST MUTATED     0  12
  IL6ST WILD-TYPE  18 325
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL6ST MUTATED      0   12
  IL6ST WILD-TYPE   18  325
                        clus
vv                       IL6ST MUTATED IL6ST WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO            12             325
[1] 2 2
[1] FALSE

Clustering(22) Variable = C19ORF55 MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  C19ORF55 MUTATED     1   4
  C19ORF55 WILD-TYPE 236 126
  C19ORF55 MUTATED C19ORF55 WILD-TYPE 
                 5                362 
  C19ORF55 MUTATED C19ORF55 WILD-TYPE 
                 4                126 
$`C19ORF55 MUTATED`
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-AADO 
        9.96        10.36        55.69        25.81        14.89 

$`C19ORF55 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MC 
        4.24         3.35         7.20         3.32         9.86        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS 
       12.00        13.12        12.56         8.61         9.14         9.86 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
        5.62        19.76         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       21.70        30.97        26.37        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        40.08        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       20.91         0.39        29.52        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       25.08        26.63        25.78        50.33        35.08        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       89.69        82.62        59.93        72.39        80.71        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        60.99 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        9.73         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.39        13.68        51.06        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
       22.95        24.46        20.42        17.10        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       11.87        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  C19ORF55 MUTATED C19ORF55 WILD-TYPE 
              9.96               0.03 
  C19ORF55 MUTATED C19ORF55 WILD-TYPE 
             55.69             120.82 
  C19ORF55 MUTATED C19ORF55 WILD-TYPE 
            14.890             19.775 
[1] "10.0 - 55.7 (14.9)" "0.0 - 120.8 (19.8)"
[1] "hr=" "2.5"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  C19ORF55 MUTATED         4        0         0          2          0
  C19ORF55 WILD-TYPE     170       86         3         62          9
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  C19ORF55 MUTATED            0        0         0         0
  C19ORF55 WILD-TYPE          9        2         1         2
D22V3, multiclass
            clus
vv           C19ORF55 MUTATED C19ORF55 WILD-TYPE
  STAGE I                   4                170
  STAGE II                  0                 86
  STAGE III                 0                  3
  STAGE IIIA                2                 62
  STAGE IIIB                0                  9
  STAGE IIIC                0                  9
  STAGE IV                  0                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C19ORF55 MUTATED     4   0   2   0
  C19ORF55 WILD-TYPE 180  94  77  13
D22V4, multiclass
    clus
vv   C19ORF55 MUTATED C19ORF55 WILD-TYPE
  T1                4                180
  T2                0                 94
  T3                2                 77
  T4                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V5, binary
                    cls
clus                   0   1
  C19ORF55 MUTATED     3   0
  C19ORF55 WILD-TYPE 251   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF55 MUTATED      3    0
  C19ORF55 WILD-TYPE  251    4
   clus
vv  C19ORF55 MUTATED C19ORF55 WILD-TYPE
  0                3                251
  1                0                  4
[1] 2 2
[1] FALSE
D22V6, binary
                    cls
clus                   0   1
  C19ORF55 MUTATED     5   0
  C19ORF55 WILD-TYPE 264   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF55 MUTATED      5    0
  C19ORF55 WILD-TYPE  264    4
   clus
vv  C19ORF55 MUTATED C19ORF55 WILD-TYPE
  0                5                264
  1                0                  4
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  C19ORF55 MUTATED     1   5
  C19ORF55 WILD-TYPE 120 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF55 MUTATED      1    5
  C19ORF55 WILD-TYPE  120  247
        clus
vv       C19ORF55 MUTATED C19ORF55 WILD-TYPE
  FEMALE                1                120
  MALE                  5                247
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  C19ORF55 MUTATED     5   0
  C19ORF55 WILD-TYPE 336   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF55 MUTATED      5    0
  C19ORF55 WILD-TYPE  336    9
     clus
vv    C19ORF55 MUTATED C19ORF55 WILD-TYPE
  NO                 5                336
  YES                0                  9
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  C19ORF55 MUTATED                         0                        6
  C19ORF55 WILD-TYPE                       3                      357
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  C19ORF55 MUTATED                                  0
  C19ORF55 WILD-TYPE                                7
D22V9, multiclass
                                  clus
vv                                 C19ORF55 MUTATED C19ORF55 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  3
  HEPATOCELLULAR CARCINOMA                        6                357
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C19ORF55 MUTATED     5   0   0   1
  C19ORF55 WILD-TYPE 322  16   1  21
D22V10, multiclass
    clus
vv   C19ORF55 MUTATED C19ORF55 WILD-TYPE
  R0                5                322
  R1                0                 16
  R2                0                  1
  RX                1                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C19ORF55 MUTATED                                  0     3
  C19ORF55 WILD-TYPE                                2   157
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C19ORF55 MUTATED                           0     3
  C19ORF55 WILD-TYPE                        17   181
D22V11, multiclass
                                  clus
vv                                 C19ORF55 MUTATED C19ORF55 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           3                157
  BLACK OR AFRICAN AMERICAN                       0                 17
  WHITE                                           3                181
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V12, binary
                    cls
clus                   0   1
  C19ORF55 MUTATED     0   6
  C19ORF55 WILD-TYPE  18 331
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF55 MUTATED      0    6
  C19ORF55 WILD-TYPE   18  331
                        clus
vv                       C19ORF55 MUTATED C19ORF55 WILD-TYPE
  HISPANIC OR LATINO                    0                 18
  NOT HISPANIC OR LATINO                6                331
[1] 2 2
[1] FALSE

Clustering(23) Variable = PIK3CA MUTATION ANALYSIS
D23V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED     9   4
  PIK3CA WILD-TYPE 228 126
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              13              354 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               4              126 
$`PIK3CA MUTATED`
TCGA-BC-A112 TCGA-ZS-A9CE TCGA-CC-5259 TCGA-DD-A1EE TCGA-DD-A3A1 TCGA-DD-AACM 
        5.03        40.80         8.22        11.47         7.66        58.16 
TCGA-DD-AACT TCGA-DD-AAD0 TCGA-DD-AADI TCGA-G3-A25U TCGA-G3-A7M8 TCGA-G3-AAV0 
       51.35         4.50        35.67        53.79        14.14        15.65 
TCGA-HP-A5N0 
       37.71 

$`PIK3CA WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-2Y-A9GS 
        7.04        10.32        44.02        29.52         0.69        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
      120.82        40.41        56.91        49.84        47.74        18.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       20.81        22.92         1.18         8.55        13.02        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 
       10.59         0.66        17.10        14.76         1.51        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.38         1.12        44.42        45.93         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       14.60        18.48        44.81        13.45         0.66         4.24 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 
        2.86         3.19         3.39         4.24         3.35         7.20 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.32         9.86         9.96        10.36        11.93        11.41 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
        9.99         8.94         7.13        21.34         9.83        12.00 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT 
       13.12        12.56         8.61         9.14         9.86         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 
       11.31         9.17         6.94         8.15        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        12.95        45.11        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       18.35        13.64        21.14        27.19        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.76        25.81        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE 
      107.11        13.78        30.61        33.14        32.52        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        26.37        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       35.67       114.35        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       76.41        55.40        12.53        71.80        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACN 
        6.41        53.19        69.11         0.30         3.52        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV 
       61.68        13.64        14.20        59.31        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD1 TCGA-DD-AAD2 
       46.82         5.59        47.67         5.62        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADJ 
       13.97        40.47        39.52         3.78        37.64        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       34.49        20.91         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
       14.33        66.67        15.58        18.21        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        89.69        82.62        59.93        72.39 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        60.99        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        20.61        19.59         0.62        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 
       14.40        60.89        23.97        19.10        27.88        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V 
        0.03         0.33         0.39        13.68        51.06        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       25.25        22.95        24.46        20.42        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       20.78        11.87        15.78        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        0.89        11.64         2.14        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 
        2.20         2.99        17.06        16.83        11.80        27.25 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       29.79        13.97        12.03         9.57        16.67        22.95 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         7.53        10.85        58.88        26.27        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 
       21.01         3.09         0.72         0.49         0.30        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       19.33        19.04        15.39        15.52        36.10        27.88 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L 
       19.76        16.44         1.71        15.98        10.75        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD 
        0.99        12.99        20.22        24.85        18.28        33.86 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       30.41        22.78        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.87        25.15        12.99        45.57        79.30        11.21 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            4.50             0.03 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           58.16           120.82 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          15.650           19.775 
[1] "4.5 - 58.2 (15.7)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.1"
D23V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PIK3CA MUTATED         6        2         0          2          0          1
  PIK3CA WILD-TYPE     168       84         3         62          9          8
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  PIK3CA MUTATED          0         0         0
  PIK3CA WILD-TYPE        2         1         2
D23V3, multiclass
            clus
vv           PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                 6              168
  STAGE II                2               84
  STAGE III               0                3
  STAGE IIIA              2               62
  STAGE IIIB              0                9
  STAGE IIIC              1                8
  STAGE IV                0                2
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PIK3CA MUTATED     6   2   3   1
  PIK3CA WILD-TYPE 178  92  76  12
D23V4, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T1              6              178
  T2              2               92
  T3              3               76
  T4              1               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V5, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     9   0
  PIK3CA WILD-TYPE 245   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      9    0
  PIK3CA WILD-TYPE  245    4
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0              9              245
  1              0                4
[1] 2 2
[1] FALSE
D23V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    10   0
  PIK3CA WILD-TYPE 259   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     10    0
  PIK3CA WILD-TYPE  259    4
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0             10              259
  1              0                4
[1] 2 2
[1] FALSE
D23V7, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     7   6
  PIK3CA WILD-TYPE 114 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      7    6
  PIK3CA WILD-TYPE  114  246
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE              7              114
  MALE                6              246
[1] 2 2
[1] FALSE
D23V8, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    13   0
  PIK3CA WILD-TYPE 328   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     13    0
  PIK3CA WILD-TYPE  328    9
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO              13              328
  YES              0                9
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  PIK3CA MUTATED                         0                       13
  PIK3CA WILD-TYPE                       3                      350
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  PIK3CA MUTATED                                  0
  PIK3CA WILD-TYPE                                7
D23V9, multiclass
                                  clus
vv                                 PIK3CA MUTATED PIK3CA WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                3
  HEPATOCELLULAR CARCINOMA                     13              350
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PIK3CA MUTATED    12   0   0   1
  PIK3CA WILD-TYPE 315  16   1  21
D23V10, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  R0             12              315
  R1              0               16
  R2              0                1
  RX              1               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3CA MUTATED                                  0     8
  PIK3CA WILD-TYPE                                2   152
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED                           0     3
  PIK3CA WILD-TYPE                        17   181
D23V11, multiclass
                                  clus
vv                                 PIK3CA MUTATED PIK3CA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         8              152
  BLACK OR AFRICAN AMERICAN                     0               17
  WHITE                                         3              181
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V12, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     0  11
  PIK3CA WILD-TYPE  18 326
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      0   11
  PIK3CA WILD-TYPE   18  326
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO             11              326
[1] 2 2
[1] FALSE

Clustering(24) Variable = CELA1 MUTATION ANALYSIS
D24V1, survival
                 sevent
clus2               0   1
  CELA1 MUTATED     3   3
  CELA1 WILD-TYPE 234 127
  CELA1 MUTATED CELA1 WILD-TYPE 
              6             361 
  CELA1 MUTATED CELA1 WILD-TYPE 
              3             127 
$`CELA1 MUTATED`
TCGA-DD-A11A TCGA-DD-A1EA TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-AACH TCGA-FV-A2QR 
        2.60        79.40        12.95        49.15         6.41        19.10 

$`CELA1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       21.34         9.83        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
        9.14         9.86         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.15        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EB 
        7.33         0.46        21.76        51.29        90.71        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.79        75.65        11.47        45.11         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       18.35        13.64        21.14        27.19        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       21.70        30.97        26.37        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       15.42        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       42.81        61.68        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
        0.39        29.52        14.89        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       25.08        26.63        25.78        50.33        35.08        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       89.69        82.62        59.93        72.39        80.71        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        60.99 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        9.73         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
       23.97        27.88        12.03         0.03         0.33         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z 
       13.68        51.06        53.79        28.27        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        25.25        22.95 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       24.46        20.42        17.10        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        0.89        11.64         2.14        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       27.25        29.79        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       22.95        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       17.69        21.01         3.09         0.72         0.49         0.30 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.04        19.33        19.04        15.39        15.52        36.10 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       27.88        19.76        16.44         1.71        15.98        10.75 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       11.34         0.99        12.99        20.22        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        22.78        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.21        35.87        25.15        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  CELA1 MUTATED CELA1 WILD-TYPE 
           2.60            0.03 
  CELA1 MUTATED CELA1 WILD-TYPE 
          79.40          120.82 
  CELA1 MUTATED CELA1 WILD-TYPE 
         16.025          19.790 
[1] "2.6 - 79.4 (16.0)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.5"
D24V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CELA1 MUTATED         3        2         1          0          0          0
  CELA1 WILD-TYPE     171       84         2         64          9          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  CELA1 MUTATED          0         0         0
  CELA1 WILD-TYPE        2         1         2
D24V3, multiclass
            clus
vv           CELA1 MUTATED CELA1 WILD-TYPE
  STAGE I                3             171
  STAGE II               2              84
  STAGE III              1               2
  STAGE IIIA             0              64
  STAGE IIIB             0               9
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CELA1 MUTATED     3   2   1   0
  CELA1 WILD-TYPE 181  92  78  13
D24V4, multiclass
    clus
vv   CELA1 MUTATED CELA1 WILD-TYPE
  T1             3             181
  T2             2              92
  T3             1              78
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V5, binary
                 cls
clus                0   1
  CELA1 MUTATED     6   0
  CELA1 WILD-TYPE 248   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CELA1 MUTATED      6    0
  CELA1 WILD-TYPE  248    4
   clus
vv  CELA1 MUTATED CELA1 WILD-TYPE
  0             6             248
  1             0               4
[1] 2 2
[1] FALSE
D24V6, binary
                 cls
clus                0   1
  CELA1 MUTATED     6   0
  CELA1 WILD-TYPE 263   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CELA1 MUTATED      6    0
  CELA1 WILD-TYPE  263    4
   clus
vv  CELA1 MUTATED CELA1 WILD-TYPE
  0             6             263
  1             0               4
[1] 2 2
[1] FALSE
D24V7, binary
                 cls
clus                0   1
  CELA1 MUTATED     1   5
  CELA1 WILD-TYPE 120 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CELA1 MUTATED      1    5
  CELA1 WILD-TYPE  120  247
        clus
vv       CELA1 MUTATED CELA1 WILD-TYPE
  FEMALE             1             120
  MALE               5             247
[1] 2 2
[1] FALSE
D24V8, binary
                 cls
clus                0   1
  CELA1 MUTATED     4   0
  CELA1 WILD-TYPE 337   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CELA1 MUTATED      4    0
  CELA1 WILD-TYPE  337    9
     clus
vv    CELA1 MUTATED CELA1 WILD-TYPE
  NO              4             337
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  CELA1 MUTATED                         0                        6
  CELA1 WILD-TYPE                       3                      357
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  CELA1 MUTATED                                  0
  CELA1 WILD-TYPE                                7
D24V9, multiclass
                                  clus
vv                                 CELA1 MUTATED CELA1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                     6             357
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CELA1 MUTATED     5   0   0   1
  CELA1 WILD-TYPE 322  16   1  21
D24V10, multiclass
    clus
vv   CELA1 MUTATED CELA1 WILD-TYPE
  R0             5             322
  R1             0              16
  R2             0               1
  RX             1              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CELA1 MUTATED                                  0     2
  CELA1 WILD-TYPE                                2   158
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CELA1 MUTATED                           1     3
  CELA1 WILD-TYPE                        16   181
D24V11, multiclass
                                  clus
vv                                 CELA1 MUTATED CELA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        2             158
  BLACK OR AFRICAN AMERICAN                    1              16
  WHITE                                        3             181
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V12, binary
                 cls
clus                0   1
  CELA1 MUTATED     0   6
  CELA1 WILD-TYPE  18 331
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CELA1 MUTATED      0    6
  CELA1 WILD-TYPE   18  331
                        clus
vv                       CELA1 MUTATED CELA1 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             6             331
[1] 2 2
[1] FALSE

Clustering(25) Variable = RPS6KA3 MUTATION ANALYSIS
D25V1, survival
                   sevent
clus2                 0   1
  RPS6KA3 MUTATED     8   6
  RPS6KA3 WILD-TYPE 229 124
  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
               14               353 
  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
                6               124 
$`RPS6KA3 MUTATED`
TCGA-2Y-A9GY TCGA-2Y-A9HB TCGA-BC-A3KG TCGA-CC-A9FW TCGA-DD-A1EE TCGA-DD-A1EH 
       24.89         8.55        22.36         8.15        11.47        49.15 
TCGA-DD-A39W TCGA-DD-AACP TCGA-DD-AAEI TCGA-DD-AAW3 TCGA-ED-A66Y TCGA-ED-A8O5 
       27.19        13.64        50.33        53.69         9.73        13.35 
TCGA-FV-A23B TCGA-ZP-A9CV 
       60.89        35.77 

$`RPS6KA3 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-3K-AAZ8 TCGA-5C-A9VG 
       18.25        20.81        22.92         1.18        13.02        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 
       10.59         0.66        17.10        14.76         1.51        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A69H 
       23.38         1.12        44.42        45.93         0.26        14.60 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 
       18.48        44.81        13.45         0.66         4.24         8.22 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 
        2.86         3.19         3.39         4.24         3.35         7.20 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.32         9.86         9.96        10.36        11.93        11.41 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
        9.99         8.94         7.13        21.34         9.83        12.00 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT 
       13.12        12.56         8.61         9.14         9.86         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
       11.31         9.17         6.94        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.33       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       12.95        45.11         6.02        33.04        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       30.61        33.14        32.52        21.70        30.97        26.37 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        71.80        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       69.11         0.30         3.52        58.16        42.81        61.68 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       14.20        59.31        51.35        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.05        34.49        20.91         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        23.74        15.72        25.08        26.63        25.78 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        89.69        82.62        59.93        72.39 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       65.39        60.99        29.92        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
       13.35         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.41         1.84         0.20        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A2QR 
       19.59         0.62        11.93        14.40        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S 
       27.88        12.03         0.03         0.33         0.39        13.68 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       51.06        53.79        28.27        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
        5.92        19.53        19.23        25.25        22.95        24.46 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       20.42        17.10        14.70        20.78        11.87        14.14 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       15.78        15.65        11.80        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       11.64         2.14        11.87        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 
        2.99        37.71        17.06        16.83        11.80        27.25 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       29.79        13.97        12.03         9.57        16.67        22.95 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         7.53        10.85        58.88        26.27        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 
       21.01         3.09         0.72         0.49         0.30        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       19.33        19.04        15.39        15.52        36.10        27.88 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L 
       19.76        16.44         1.71        15.98        10.75        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD 
        0.99        12.99        20.22        24.85        18.28        33.86 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       30.41        22.78        13.55        25.71        23.21        35.87 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        79.30        11.21 

  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
             8.15              0.03 
  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
            60.89            120.82 
  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
           23.625            19.760 
[1] "8.2 - 60.9 (23.6)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.2"
D25V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  RPS6KA3 MUTATED         4        3         2          4          0          0
  RPS6KA3 WILD-TYPE     170       83         1         60          9          9
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  RPS6KA3 MUTATED          0         0         0
  RPS6KA3 WILD-TYPE        2         1         2
D25V3, multiclass
            clus
vv           RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  STAGE I                  4               170
  STAGE II                 3                83
  STAGE III                2                 1
  STAGE IIIA               4                60
  STAGE IIIB               0                 9
  STAGE IIIC               0                 9
  STAGE IV                 0                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RPS6KA3 MUTATED     5   3   6   0
  RPS6KA3 WILD-TYPE 179  91  73  13
D25V4, multiclass
    clus
vv   RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  T1               5               179
  T2               3                91
  T3               6                73
  T4               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V5, binary
                   cls
clus                  0   1
  RPS6KA3 MUTATED    11   0
  RPS6KA3 WILD-TYPE 243   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA3 MUTATED     11    0
  RPS6KA3 WILD-TYPE  243    4
   clus
vv  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  0              11               243
  1               0                 4
[1] 2 2
[1] FALSE
D25V6, binary
                   cls
clus                  0   1
  RPS6KA3 MUTATED    11   0
  RPS6KA3 WILD-TYPE 258   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA3 MUTATED     11    0
  RPS6KA3 WILD-TYPE  258    4
   clus
vv  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  0              11               258
  1               0                 4
[1] 2 2
[1] FALSE
D25V7, binary
                   cls
clus                  0   1
  RPS6KA3 MUTATED     6   8
  RPS6KA3 WILD-TYPE 115 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA3 MUTATED      6    8
  RPS6KA3 WILD-TYPE  115  244
        clus
vv       RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  FEMALE               6               115
  MALE                 8               244
[1] 2 2
[1] FALSE
D25V8, binary
                   cls
clus                  0   1
  RPS6KA3 MUTATED    13   0
  RPS6KA3 WILD-TYPE 328   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA3 MUTATED     13    0
  RPS6KA3 WILD-TYPE  328    9
     clus
vv    RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  NO               13               328
  YES               0                 9
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  RPS6KA3 MUTATED                         0                       14
  RPS6KA3 WILD-TYPE                       3                      349
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  RPS6KA3 MUTATED                                  0
  RPS6KA3 WILD-TYPE                                7
D25V9, multiclass
                                  clus
vv                                 RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 3
  HEPATOCELLULAR CARCINOMA                      14               349
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  RPS6KA3 MUTATED    14   0   0   0
  RPS6KA3 WILD-TYPE 313  16   1  22
D25V10, multiclass
    clus
vv   RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  R0              14               313
  R1               0                16
  R2               0                 1
  RX               0                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPS6KA3 MUTATED                                  0     6
  RPS6KA3 WILD-TYPE                                2   154
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  RPS6KA3 MUTATED                           0     7
  RPS6KA3 WILD-TYPE                        17   177
D25V11, multiclass
                                  clus
vv                                 RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          6               154
  BLACK OR AFRICAN AMERICAN                      0                17
  WHITE                                          7               177
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V12, binary
                   cls
clus                  0   1
  RPS6KA3 MUTATED     1  13
  RPS6KA3 WILD-TYPE  17 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA3 MUTATED      1   13
  RPS6KA3 WILD-TYPE   17  324
                        clus
vv                       RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  HISPANIC OR LATINO                   1                17
  NOT HISPANIC OR LATINO              13               324
[1] 2 2
[1] FALSE

Clustering(26) Variable = NRD1 MUTATION ANALYSIS
D26V1, survival
                sevent
clus2              0   1
  NRD1 MUTATED     6   6
  NRD1 WILD-TYPE 231 124
  NRD1 MUTATED NRD1 WILD-TYPE 
            12            355 
  NRD1 MUTATED NRD1 WILD-TYPE 
             6            124 
$`NRD1 MUTATED`
TCGA-G3-A3CG TCGA-2Y-A9HA TCGA-BC-A3KF TCGA-CC-A1HT TCGA-CC-A3MA TCGA-DD-A39X 
       22.13         1.18         0.26         3.32         9.96        55.69 
TCGA-DD-A3A7 TCGA-DD-AAVV TCGA-EP-A12J TCGA-FV-A2QR TCGA-G3-A3CK TCGA-RC-A6M5 
       13.78        80.71        18.74        19.10        19.23         0.49 

$`NRD1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A6UC TCGA-G3-A7M9 
        8.12         6.38        81.73        30.74        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       18.25        20.81        22.92         8.55        13.02        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 
       10.59         0.66        17.10        14.76         1.51        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H 
       23.38         1.12        44.42        45.93        22.36        14.60 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 
       18.48        44.81        13.45         0.66         4.24         8.22 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 
        2.86         3.19         3.39         4.24         3.35         7.20 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE 
        9.86        10.36        11.93        11.41         9.99         8.94 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ 
        7.13        21.34         9.83        12.00        13.12        12.56 
TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
        8.61         9.14         9.86         4.60        11.31         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        6.94         8.15        79.73        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
      113.00         7.33         2.60         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65        11.47 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        33.04        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        27.19         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       30.61        33.14        32.52        21.70        30.97        26.37 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        71.80        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       69.11         0.30         3.52        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV 
       13.64        14.20        59.31        51.35        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       46.82         5.59        47.67         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        42.58        44.22        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.83        13.97        40.47        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       35.67        35.05        34.49        20.91         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       14.89        15.06        14.33        66.67        15.58        18.21 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       19.30        18.25        18.25        18.15        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       19.99         4.64        23.74        15.72        25.08        26.63 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       25.78        50.33        35.08        90.48        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       59.93        72.39        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        60.99        53.69        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       28.08        13.91        13.35         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20        14.04        13.15        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
        0.20        19.99        20.61        19.59         0.62        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       14.40        60.89        23.97        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SI 
       14.86        21.53        25.64         5.92        19.53        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
       22.95        24.46        20.42        17.10        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       11.87        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M6 
       26.27        17.69        21.01         3.09         0.72         0.30 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.04        19.33        19.04        15.39        15.52        36.10 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       27.88        19.76        16.44         1.71        15.98        10.75 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       11.34         0.99        12.99        20.22        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        22.78        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.21        35.87        25.15        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  NRD1 MUTATED NRD1 WILD-TYPE 
          0.26           0.03 
  NRD1 MUTATED NRD1 WILD-TYPE 
         80.71         120.82 
  NRD1 MUTATED NRD1 WILD-TYPE 
         16.26          19.99 
[1] "0.3 - 80.7 (16.3)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "2"  
D26V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  NRD1 MUTATED         6        3         0          2          1          0
  NRD1 WILD-TYPE     168       83         3         62          8          9
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  NRD1 MUTATED          0         1         0
  NRD1 WILD-TYPE        2         0         2
D26V3, multiclass
            clus
vv           NRD1 MUTATED NRD1 WILD-TYPE
  STAGE I               6            168
  STAGE II              3             83
  STAGE III             0              3
  STAGE IIIA            2             62
  STAGE IIIB            1              8
  STAGE IIIC            0              9
  STAGE IV              0              2
  STAGE IVA             1              0
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NRD1 MUTATED     7   3   3   0
  NRD1 WILD-TYPE 177  91  76  13
D26V4, multiclass
    clus
vv   NRD1 MUTATED NRD1 WILD-TYPE
  T1            7            177
  T2            3             91
  T3            3             76
  T4            0             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V5, binary
                cls
clus               0   1
  NRD1 MUTATED     8   1
  NRD1 WILD-TYPE 246   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRD1 MUTATED      8    1
  NRD1 WILD-TYPE  246    3
   clus
vv  NRD1 MUTATED NRD1 WILD-TYPE
  0            8            246
  1            1              3
[1] 2 2
[1] FALSE
D26V6, binary
                cls
clus               0   1
  NRD1 MUTATED    11   0
  NRD1 WILD-TYPE 258   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRD1 MUTATED     11    0
  NRD1 WILD-TYPE  258    4
   clus
vv  NRD1 MUTATED NRD1 WILD-TYPE
  0           11            258
  1            0              4
[1] 2 2
[1] FALSE
D26V7, binary
                cls
clus               0   1
  NRD1 MUTATED     3  10
  NRD1 WILD-TYPE 118 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRD1 MUTATED      3   10
  NRD1 WILD-TYPE  118  242
        clus
vv       NRD1 MUTATED NRD1 WILD-TYPE
  FEMALE            3            118
  MALE             10            242
[1] 2 2
[1] FALSE
D26V8, binary
                cls
clus               0   1
  NRD1 MUTATED    10   0
  NRD1 WILD-TYPE 331   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRD1 MUTATED     10    0
  NRD1 WILD-TYPE  331    9
     clus
vv    NRD1 MUTATED NRD1 WILD-TYPE
  NO            10            331
  YES            0              9
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  NRD1 MUTATED                         1                       12
  NRD1 WILD-TYPE                       2                      351
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  NRD1 MUTATED                                  0
  NRD1 WILD-TYPE                                7
D26V9, multiclass
                                  clus
vv                                 NRD1 MUTATED NRD1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     1              2
  HEPATOCELLULAR CARCINOMA                   12            351
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NRD1 MUTATED    10   1   0   1
  NRD1 WILD-TYPE 317  15   1  21
D26V10, multiclass
    clus
vv   NRD1 MUTATED NRD1 WILD-TYPE
  R0           10            317
  R1            1             15
  R2            0              1
  RX            1             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NRD1 MUTATED                                  1     4
  NRD1 WILD-TYPE                                1   156
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NRD1 MUTATED                           1     6
  NRD1 WILD-TYPE                        16   178
D26V11, multiclass
                                  clus
vv                                 NRD1 MUTATED NRD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              1
  ASIAN                                       4            156
  BLACK OR AFRICAN AMERICAN                   1             16
  WHITE                                       6            178
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V12, binary
                cls
clus               0   1
  NRD1 MUTATED     0   9
  NRD1 WILD-TYPE  18 328
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRD1 MUTATED      0    9
  NRD1 WILD-TYPE   18  328
                        clus
vv                       NRD1 MUTATED NRD1 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            9            328
[1] 2 2
[1] FALSE

Clustering(27) Variable = EEF1A1 MUTATION ANALYSIS
D27V1, survival
                  sevent
clus2                0   1
  EEF1A1 MUTATED     4   5
  EEF1A1 WILD-TYPE 233 125
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
               9              358 
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
               5              125 
$`EEF1A1 MUTATED`
TCGA-KR-A7K0 TCGA-2Y-A9GT TCGA-DD-A11B TCGA-DD-AACK TCGA-DD-AAD8 TCGA-G3-A25V 
        2.14        53.39         0.46         0.30        40.08        28.27 
TCGA-UB-A7MD TCGA-YA-A8S7 TCGA-ZP-A9CY 
        1.71        13.55        25.71 

$`EEF1A1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
        1.84        20.75        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       23.80        63.75        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
      120.82        40.41        56.91        49.84        47.74        18.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       20.81        22.92         1.18         8.55        13.02        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 
       10.59         0.66        17.10        14.76         1.51        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.38         1.12        44.42        45.93         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       14.60        18.48        44.81        13.45         0.66         4.24 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
        8.22         2.86         3.19         3.39         4.24         3.35 
TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        7.20         3.32         9.86         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS 
       12.00        13.12        12.56         8.61         9.14         9.86 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65        11.47        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ 
       32.52        21.70        30.97        26.37        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACL 
       12.00        15.42         6.41        53.19        69.11         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       22.09        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
        0.39        29.52        14.89        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       25.08        26.63        25.78        50.33        35.08        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       89.69        82.62        59.93        72.39        80.71        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        60.99 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        9.73         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25Y TCGA-G3-A25Z 
        0.39        13.68        51.06        53.79        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        25.25        22.95 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       24.46        20.42        17.10        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        0.89        11.64         2.14        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       27.25        29.79        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       22.95        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       17.69        21.01         3.09         0.72         0.49         0.30 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.04        19.33        19.04        15.39        15.52        36.10 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L 
       27.88        19.76        16.44        15.98        10.75        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD 
        0.99        12.99        20.22        24.85        18.28        33.86 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-ZP-A9CV TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       30.41        22.78        35.77        23.21        35.87        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        79.30        11.21 

  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
            0.30             0.03 
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
           53.39           120.82 
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
          13.550           19.775 
[1] "0.3 - 53.4 (13.6)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "2.3"
D27V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  EEF1A1 MUTATED         7        0         0          1          0          0
  EEF1A1 WILD-TYPE     167       86         3         63          9          9
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  EEF1A1 MUTATED          0         0         0
  EEF1A1 WILD-TYPE        2         1         2
D27V3, multiclass
            clus
vv           EEF1A1 MUTATED EEF1A1 WILD-TYPE
  STAGE I                 7              167
  STAGE II                0               86
  STAGE III               0                3
  STAGE IIIA              1               63
  STAGE IIIB              0                9
  STAGE IIIC              0                9
  STAGE IV                0                2
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  EEF1A1 MUTATED     8   0   1   0
  EEF1A1 WILD-TYPE 176  94  78  13
D27V4, multiclass
    clus
vv   EEF1A1 MUTATED EEF1A1 WILD-TYPE
  T1              8              176
  T2              0               94
  T3              1               78
  T4              0               13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V5, binary
                  cls
clus                 0   1
  EEF1A1 MUTATED     7   0
  EEF1A1 WILD-TYPE 247   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EEF1A1 MUTATED      7    0
  EEF1A1 WILD-TYPE  247    4
   clus
vv  EEF1A1 MUTATED EEF1A1 WILD-TYPE
  0              7              247
  1              0                4
[1] 2 2
[1] FALSE
D27V6, binary
                  cls
clus                 0   1
  EEF1A1 MUTATED     5   0
  EEF1A1 WILD-TYPE 264   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EEF1A1 MUTATED      5    0
  EEF1A1 WILD-TYPE  264    4
   clus
vv  EEF1A1 MUTATED EEF1A1 WILD-TYPE
  0              5              264
  1              0                4
[1] 2 2
[1] FALSE
D27V7, binary
                  cls
clus                 0   1
  EEF1A1 MUTATED     2   7
  EEF1A1 WILD-TYPE 119 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EEF1A1 MUTATED      2    7
  EEF1A1 WILD-TYPE  119  245
        clus
vv       EEF1A1 MUTATED EEF1A1 WILD-TYPE
  FEMALE              2              119
  MALE                7              245
[1] 2 2
[1] FALSE
D27V8, binary
                  cls
clus                 0   1
  EEF1A1 MUTATED     9   0
  EEF1A1 WILD-TYPE 332   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EEF1A1 MUTATED      9    0
  EEF1A1 WILD-TYPE  332    9
     clus
vv    EEF1A1 MUTATED EEF1A1 WILD-TYPE
  NO               9              332
  YES              0                9
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  EEF1A1 MUTATED                         0                        9
  EEF1A1 WILD-TYPE                       3                      354
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  EEF1A1 MUTATED                                  0
  EEF1A1 WILD-TYPE                                7
D27V9, multiclass
                                  clus
vv                                 EEF1A1 MUTATED EEF1A1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                3
  HEPATOCELLULAR CARCINOMA                      9              354
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  EEF1A1 MUTATED     8   0   0   1
  EEF1A1 WILD-TYPE 319  16   1  21
D27V10, multiclass
    clus
vv   EEF1A1 MUTATED EEF1A1 WILD-TYPE
  R0              8              319
  R1              0               16
  R2              0                1
  RX              1               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EEF1A1 MUTATED                                  0     2
  EEF1A1 WILD-TYPE                                2   158
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  EEF1A1 MUTATED                           1     6
  EEF1A1 WILD-TYPE                        16   178
D27V11, multiclass
                                  clus
vv                                 EEF1A1 MUTATED EEF1A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         2              158
  BLACK OR AFRICAN AMERICAN                     1               16
  WHITE                                         6              178
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V12, binary
                  cls
clus                 0   1
  EEF1A1 MUTATED     1   7
  EEF1A1 WILD-TYPE  17 330
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EEF1A1 MUTATED      1    7
  EEF1A1 WILD-TYPE   17  330
                        clus
vv                       EEF1A1 MUTATED EEF1A1 WILD-TYPE
  HISPANIC OR LATINO                  1               17
  NOT HISPANIC OR LATINO              7              330
[1] 2 2
[1] FALSE

Clustering(28) Variable = TCHH MUTATION ANALYSIS
D28V1, survival
                sevent
clus2              0   1
  TCHH MUTATED    11   6
  TCHH WILD-TYPE 226 124
  TCHH MUTATED TCHH WILD-TYPE 
            17            350 
  TCHH MUTATED TCHH WILD-TYPE 
             6            124 
$`TCHH MUTATED`
TCGA-ZP-A9D1 TCGA-5C-A9VG TCGA-CC-5259 TCGA-CC-A5UE TCGA-CC-A7IH TCGA-DD-A1EK 
        0.69        10.78         8.22         8.94        12.00        18.35 
TCGA-DD-A3A2 TCGA-DD-A4NN TCGA-DD-AAC9 TCGA-DD-AACN TCGA-DD-AAD5 TCGA-DD-AADO 
       70.06        29.56        11.41        42.81        44.22        14.89 
TCGA-DD-AAVU TCGA-DD-AAW2 TCGA-G3-A5SI TCGA-O8-A75V TCGA-XR-A8TF 
       72.39        60.99        25.25        17.69        22.78 

$`TCHH WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZS-A9CE 
        0.76         7.04        10.32        44.02        29.52        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        20.81        22.92         1.18         8.55        13.02 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 
       10.59         0.66        17.10        14.76         1.51        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.38         1.12        44.42        45.93         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       14.60        18.48        44.81        13.45         0.66         4.24 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 
        2.86         3.19         3.39         4.24         3.35         7.20 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.32         9.86         9.96        10.36        11.93        11.41 
TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ 
        9.99         7.13        21.34         9.83        13.12        12.56 
TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
        8.61         9.14         9.86         4.60        11.31         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        6.94         8.15        79.73        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
      113.00         7.33         2.60         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65        11.47 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL 
       12.95        45.11        49.15         6.02        33.04        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       21.14        27.19        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
        7.66        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       30.61        33.14        32.52        21.70        30.97        26.37 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NP 
       30.15        30.51        39.78        56.25        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       23.05        22.78         1.45        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
        0.53        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
        3.52        58.16        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 
        5.62         4.50        18.54        21.63        42.58        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
        0.39        29.52        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.21        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
       18.61        19.99         4.64        23.74        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       26.63        25.78        50.33        35.08        90.48        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       82.62        59.93        80.71        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       62.47        66.25        65.39        53.69        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       28.08        13.91        13.35         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20        14.04        13.15        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        20.61        19.59         0.62 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        19.23        22.95        24.46        20.42        17.10 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       14.70        20.78        11.87        14.14        15.78        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80        12.23        13.55         0.89        11.64         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        28.90         1.02         2.20         2.99        37.71 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06        16.83        11.80        27.25        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       10.85        58.88        26.27        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-YA-A8S7 TCGA-ZP-A9CV 
       24.85        18.28        33.86        30.41        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  TCHH MUTATED TCHH WILD-TYPE 
          0.69           0.03 
  TCHH MUTATED TCHH WILD-TYPE 
         72.39         120.82 
  TCHH MUTATED TCHH WILD-TYPE 
        18.350         19.775 
[1] "0.7 - 72.4 (18.4)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1"  
D28V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TCHH MUTATED         9        3         0          1          1          1
  TCHH WILD-TYPE     165       83         3         63          8          8
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  TCHH MUTATED          0         0         1
  TCHH WILD-TYPE        2         1         1
D28V3, multiclass
            clus
vv           TCHH MUTATED TCHH WILD-TYPE
  STAGE I               9            165
  STAGE II              3             83
  STAGE III             0              3
  STAGE IIIA            1             63
  STAGE IIIB            1              8
  STAGE IIIC            1              8
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             1              1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TCHH MUTATED    10   3   1   3
  TCHH WILD-TYPE 174  91  78  10
D28V4, multiclass
    clus
vv   TCHH MUTATED TCHH WILD-TYPE
  T1           10            174
  T2            3             91
  T3            1             78
  T4            3             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V5, binary
                cls
clus               0   1
  TCHH MUTATED    14   0
  TCHH WILD-TYPE 240   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHH MUTATED     14    0
  TCHH WILD-TYPE  240    4
   clus
vv  TCHH MUTATED TCHH WILD-TYPE
  0           14            240
  1            0              4
[1] 2 2
[1] FALSE
D28V6, binary
                cls
clus               0   1
  TCHH MUTATED    13   1
  TCHH WILD-TYPE 256   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHH MUTATED     13    1
  TCHH WILD-TYPE  256    3
   clus
vv  TCHH MUTATED TCHH WILD-TYPE
  0           13            256
  1            1              3
[1] 2 2
[1] FALSE
D28V7, binary
                cls
clus               0   1
  TCHH MUTATED     5  12
  TCHH WILD-TYPE 116 240
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHH MUTATED      5   12
  TCHH WILD-TYPE  116  240
        clus
vv       TCHH MUTATED TCHH WILD-TYPE
  FEMALE            5            116
  MALE             12            240
[1] 2 2
[1] FALSE
D28V8, binary
                cls
clus               0   1
  TCHH MUTATED    17   0
  TCHH WILD-TYPE 324   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHH MUTATED     17    0
  TCHH WILD-TYPE  324    9
     clus
vv    TCHH MUTATED TCHH WILD-TYPE
  NO            17            324
  YES            0              9
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  TCHH MUTATED                         0                       17
  TCHH WILD-TYPE                       3                      346
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  TCHH MUTATED                                  0
  TCHH WILD-TYPE                                7
D28V9, multiclass
                                  clus
vv                                 TCHH MUTATED TCHH WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              3
  HEPATOCELLULAR CARCINOMA                   17            346
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TCHH MUTATED    16   1   0   0
  TCHH WILD-TYPE 311  15   1  22
D28V10, multiclass
    clus
vv   TCHH MUTATED TCHH WILD-TYPE
  R0           16            311
  R1            1             15
  R2            0              1
  RX            0             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TCHH MUTATED                                  0    10
  TCHH WILD-TYPE                                2   150
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TCHH MUTATED                           0     6
  TCHH WILD-TYPE                        17   178
D28V11, multiclass
                                  clus
vv                                 TCHH MUTATED TCHH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                      10            150
  BLACK OR AFRICAN AMERICAN                   0             17
  WHITE                                       6            178
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V12, binary
                cls
clus               0   1
  TCHH MUTATED     2  15
  TCHH WILD-TYPE  16 322
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCHH MUTATED      2   15
  TCHH WILD-TYPE   16  322
                        clus
vv                       TCHH MUTATED TCHH WILD-TYPE
  HISPANIC OR LATINO                2             16
  NOT HISPANIC OR LATINO           15            322
[1] 2 2
[1] FALSE

Clustering(29) Variable = COG2 MUTATION ANALYSIS
D29V1, survival
                sevent
clus2              0   1
  COG2 MUTATED     1   3
  COG2 WILD-TYPE 236 127
  COG2 MUTATED COG2 WILD-TYPE 
             4            363 
  COG2 MUTATED COG2 WILD-TYPE 
             3            127 
$`COG2 MUTATED`
TCGA-DD-A1EG TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-G3-A3CJ 
       45.11         5.62        25.81        19.53 

$`COG2 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       21.34         9.83        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
        9.14         9.86         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.15        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65        11.47        12.95 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       27.19        55.69        19.76         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ 
       32.52        21.70        30.97        26.37        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       34.49        20.91         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
       14.33        66.67        15.58        18.21        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        89.69        82.62        59.93        72.39 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        60.99        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        20.61        19.59         0.62        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 
       14.40        60.89        23.97        19.10        27.88        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.03         0.33         0.39        13.68        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
       28.27        14.86        21.53        25.64         5.92        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       25.25        22.95        24.46        20.42        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       20.78        11.87        14.14        15.78        15.65        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       12.23        13.55         0.89        11.64         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       58.88        26.27        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        22.78        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        25.71        23.21        35.87        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  COG2 MUTATED COG2 WILD-TYPE 
          5.62           0.03 
  COG2 MUTATED COG2 WILD-TYPE 
         45.11         120.82 
  COG2 MUTATED COG2 WILD-TYPE 
         22.67          19.76 
[1] "5.6 - 45.1 (22.7)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "2.3"
D29V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  COG2 MUTATED         3        1         0          0          0          0
  COG2 WILD-TYPE     171       85         3         64          9          9
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  COG2 MUTATED          0         0         0
  COG2 WILD-TYPE        2         1         2
D29V3, multiclass
            clus
vv           COG2 MUTATED COG2 WILD-TYPE
  STAGE I               3            171
  STAGE II              1             85
  STAGE III             0              3
  STAGE IIIA            0             64
  STAGE IIIB            0              9
  STAGE IIIC            0              9
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  COG2 MUTATED     3   1   0   0
  COG2 WILD-TYPE 181  93  79  13
D29V4, multiclass
    clus
vv   COG2 MUTATED COG2 WILD-TYPE
  T1            3            181
  T2            1             93
  T3            0             79
  T4            0             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V5, binary
                cls
clus               0   1
  COG2 MUTATED     2   0
  COG2 WILD-TYPE 252   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  COG2 MUTATED      2    0
  COG2 WILD-TYPE  252    4
   clus
vv  COG2 MUTATED COG2 WILD-TYPE
  0            2            252
  1            0              4
[1] 2 2
[1] FALSE
D29V6, binary
                cls
clus               0   1
  COG2 MUTATED     4   0
  COG2 WILD-TYPE 265   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  COG2 MUTATED      4    0
  COG2 WILD-TYPE  265    4
   clus
vv  COG2 MUTATED COG2 WILD-TYPE
  0            4            265
  1            0              4
[1] 2 2
[1] FALSE
D29V7, binary
                cls
clus               0   1
  COG2 MUTATED     0   4
  COG2 WILD-TYPE 121 248
[1] "tbl2"
                cls
clus             [,1] [,2]
  COG2 MUTATED      0    4
  COG2 WILD-TYPE  121  248
        clus
vv       COG2 MUTATED COG2 WILD-TYPE
  FEMALE            0            121
  MALE              4            248
[1] 2 2
[1] FALSE
D29V8, binary
                cls
clus               0   1
  COG2 MUTATED     4   0
  COG2 WILD-TYPE 337   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  COG2 MUTATED      4    0
  COG2 WILD-TYPE  337    9
     clus
vv    COG2 MUTATED COG2 WILD-TYPE
  NO             4            337
  YES            0              9
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  COG2 MUTATED                         0                        4
  COG2 WILD-TYPE                       3                      359
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  COG2 MUTATED                                  0
  COG2 WILD-TYPE                                7
D29V9, multiclass
                                  clus
vv                                 COG2 MUTATED COG2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              3
  HEPATOCELLULAR CARCINOMA                    4            359
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  COG2 MUTATED     4   0   0   0
  COG2 WILD-TYPE 323  16   1  22
D29V10, multiclass
    clus
vv   COG2 MUTATED COG2 WILD-TYPE
  R0            4            323
  R1            0             16
  R2            0              1
  RX            0             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COG2 MUTATED                                  1     1
  COG2 WILD-TYPE                                1   159
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  COG2 MUTATED                           0     2
  COG2 WILD-TYPE                        17   182
D29V11, multiclass
                                  clus
vv                                 COG2 MUTATED COG2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              1
  ASIAN                                       1            159
  BLACK OR AFRICAN AMERICAN                   0             17
  WHITE                                       2            182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V12, binary
                cls
clus               0   1
  COG2 MUTATED     0   4
  COG2 WILD-TYPE  18 333
[1] "tbl2"
                cls
clus             [,1] [,2]
  COG2 MUTATED      0    4
  COG2 WILD-TYPE   18  333
                        clus
vv                       COG2 MUTATED COG2 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            4            333
[1] 2 2
[1] FALSE

Clustering(30) Variable = ATXN1 MUTATION ANALYSIS
D30V1, survival
                 sevent
clus2               0   1
  ATXN1 MUTATED     3   7
  ATXN1 WILD-TYPE 234 123
  ATXN1 MUTATED ATXN1 WILD-TYPE 
             10             357 
  ATXN1 MUTATED ATXN1 WILD-TYPE 
              7             123 
$`ATXN1 MUTATED`
TCGA-4R-AA8I TCGA-2Y-A9GZ TCGA-2Y-A9H1 TCGA-CC-A5UE TCGA-DD-A1EG TCGA-DD-A1EJ 
        8.61        27.88        40.41         8.94        45.11        33.04 
TCGA-DD-AACY TCGA-DD-AAVP TCGA-G3-A3CJ TCGA-HP-A5N0 
       47.67        90.48        19.53        37.71 

$`ATXN1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        11.74        38.40        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9H0 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 
      120.82        56.91        49.84        47.74        18.25        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH 
       22.92         1.18         8.55        13.02        10.78        10.59 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q 
        0.66        17.10        14.76         1.51        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       10.13        27.52        27.52         2.99        25.32        23.38 
TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        1.12        44.42        45.93         0.26        22.36        14.60 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 
       18.48        44.81        13.45         0.66         4.24         8.22 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 
        2.86         3.19         3.39         4.24         3.35         7.20 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.32         9.86         9.96        10.36        11.93        11.41 
TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II 
        9.99         7.13        21.34         9.83        12.00        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU 
       12.56         8.61         9.14         9.86         4.60        11.31 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        9.17         6.94         8.15        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.33       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL 
       11.47        12.95        49.15         6.02        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       21.14        27.19        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF 
       13.78        30.61        33.14        32.52        21.70        30.97 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       26.37        30.15        30.51        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      114.35        13.48         0.53        11.41        75.65        76.41 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        71.80        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
       53.19        69.11         0.30         3.52        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
       61.68        13.64        14.20        59.31        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       50.33        46.82         5.59         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        42.58        44.22        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.83        13.97        40.47        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       35.67        35.05        34.49        20.91         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       14.89        15.06        14.33        66.67        15.58        18.21 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       19.30        18.25        18.25        18.15        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       19.99         4.64        23.74        15.72        25.08        26.63 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       25.78        50.33        35.08        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.39        80.71        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        60.99        53.69        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       28.08        13.91        13.35         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20        14.04        13.15        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        20.61        19.59         0.62 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        14.86        21.53        25.64         5.92 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        25.25        22.95        24.46        20.42        17.10 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       14.70        20.78        11.87        14.14        15.78        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80        12.23        13.55         0.89        11.64         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RG 
       11.87        28.90         1.02         2.20         2.99        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       58.88        26.27        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        22.78        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        25.71        23.21        35.87        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  ATXN1 MUTATED ATXN1 WILD-TYPE 
           8.61            0.03 
  ATXN1 MUTATED ATXN1 WILD-TYPE 
          90.48          120.82 
  ATXN1 MUTATED ATXN1 WILD-TYPE 
         35.375          19.590 
[1] "8.6 - 90.5 (35.4)"  "0.0 - 120.8 (19.6)"
[1] "hr=" "1.5"
D30V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ATXN1 MUTATED         4        3         0          0          1          1
  ATXN1 WILD-TYPE     170       83         3         64          8          8
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  ATXN1 MUTATED          0         0         0
  ATXN1 WILD-TYPE        2         1         2
D30V3, multiclass
            clus
vv           ATXN1 MUTATED ATXN1 WILD-TYPE
  STAGE I                4             170
  STAGE II               3              83
  STAGE III              0               3
  STAGE IIIA             0              64
  STAGE IIIB             1               8
  STAGE IIIC             1               8
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ATXN1 MUTATED     5   3   0   1
  ATXN1 WILD-TYPE 179  91  79  12
D30V4, multiclass
    clus
vv   ATXN1 MUTATED ATXN1 WILD-TYPE
  T1             5             179
  T2             3              91
  T3             0              79
  T4             1              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V5, binary
                 cls
clus                0   1
  ATXN1 MUTATED     5   1
  ATXN1 WILD-TYPE 249   3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN1 MUTATED      5    1
  ATXN1 WILD-TYPE  249    3
   clus
vv  ATXN1 MUTATED ATXN1 WILD-TYPE
  0             5             249
  1             1               3
[1] 2 2
[1] FALSE
D30V6, binary
                 cls
clus                0   1
  ATXN1 MUTATED     7   0
  ATXN1 WILD-TYPE 262   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN1 MUTATED      7    0
  ATXN1 WILD-TYPE  262    4
   clus
vv  ATXN1 MUTATED ATXN1 WILD-TYPE
  0             7             262
  1             0               4
[1] 2 2
[1] FALSE
D30V7, binary
                 cls
clus                0   1
  ATXN1 MUTATED     3   7
  ATXN1 WILD-TYPE 118 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN1 MUTATED      3    7
  ATXN1 WILD-TYPE  118  245
        clus
vv       ATXN1 MUTATED ATXN1 WILD-TYPE
  FEMALE             3             118
  MALE               7             245
[1] 2 2
[1] FALSE
D30V8, binary
                 cls
clus                0   1
  ATXN1 MUTATED    10   0
  ATXN1 WILD-TYPE 331   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN1 MUTATED     10    0
  ATXN1 WILD-TYPE  331    9
     clus
vv    ATXN1 MUTATED ATXN1 WILD-TYPE
  NO             10             331
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  ATXN1 MUTATED                         0                       10
  ATXN1 WILD-TYPE                       3                      353
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  ATXN1 MUTATED                                  0
  ATXN1 WILD-TYPE                                7
D30V9, multiclass
                                  clus
vv                                 ATXN1 MUTATED ATXN1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                    10             353
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ATXN1 MUTATED    10   0   0   0
  ATXN1 WILD-TYPE 317  16   1  22
D30V10, multiclass
    clus
vv   ATXN1 MUTATED ATXN1 WILD-TYPE
  R0            10             317
  R1             0              16
  R2             0               1
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATXN1 MUTATED                                  1     3
  ATXN1 WILD-TYPE                                1   157
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ATXN1 MUTATED                           0     5
  ATXN1 WILD-TYPE                        17   179
D30V11, multiclass
                                  clus
vv                                 ATXN1 MUTATED ATXN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               1
  ASIAN                                        3             157
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        5             179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V12, binary
                 cls
clus                0   1
  ATXN1 MUTATED     0   9
  ATXN1 WILD-TYPE  18 328
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN1 MUTATED      0    9
  ATXN1 WILD-TYPE   18  328
                        clus
vv                       ATXN1 MUTATED ATXN1 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             9             328
[1] 2 2
[1] FALSE

Clustering(31) Variable = KCTD20 MUTATION ANALYSIS
D31V1, survival
                  sevent
clus2                0   1
  KCTD20 MUTATED     2   3
  KCTD20 WILD-TYPE 235 127
  KCTD20 MUTATED KCTD20 WILD-TYPE 
               5              362 
  KCTD20 MUTATED KCTD20 WILD-TYPE 
               3              127 
$`KCTD20 MUTATED`
TCGA-DD-A1EE TCGA-DD-A1EJ TCGA-DD-A3A9 TCGA-DD-A73E TCGA-DD-AAE1 
       11.47        33.04        30.61         1.45        18.15 

$`KCTD20 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       21.34         9.83        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
        9.14         9.86         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.15        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG 
       79.40        66.31        19.79        75.65        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
       49.15         6.02        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A4NA 
       17.59        20.12       102.74       107.11        13.78        33.14 
TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ 
       32.52        21.70        30.97        26.37        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
       22.78        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        40.08        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        29.52        14.89        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       66.67        15.58        18.21        19.30        18.25        18.25 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       25.08        26.63        25.78        50.33        35.08        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       89.69        82.62        59.93        72.39        80.71        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        60.99 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        9.73         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.39        13.68        51.06        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
       22.95        24.46        20.42        17.10        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       11.87        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  KCTD20 MUTATED KCTD20 WILD-TYPE 
            1.45             0.03 
  KCTD20 MUTATED KCTD20 WILD-TYPE 
           33.04           120.82 
  KCTD20 MUTATED KCTD20 WILD-TYPE 
          18.150           19.775 
[1] "1.4 - 33.0 (18.1)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "2.2"
D31V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  KCTD20 MUTATED         2        0         0          1          0          1
  KCTD20 WILD-TYPE     172       86         3         63          9          8
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  KCTD20 MUTATED          0         0         1
  KCTD20 WILD-TYPE        2         1         1
D31V3, multiclass
            clus
vv           KCTD20 MUTATED KCTD20 WILD-TYPE
  STAGE I                 2              172
  STAGE II                0               86
  STAGE III               0                3
  STAGE IIIA              1               63
  STAGE IIIB              0                9
  STAGE IIIC              1                8
  STAGE IV                0                2
  STAGE IVA               0                1
  STAGE IVB               1                1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KCTD20 MUTATED     3   0   1   1
  KCTD20 WILD-TYPE 181  94  78  12
D31V4, multiclass
    clus
vv   KCTD20 MUTATED KCTD20 WILD-TYPE
  T1              3              181
  T2              0               94
  T3              1               78
  T4              1               12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V5, binary
                  cls
clus                 0   1
  KCTD20 MUTATED     4   1
  KCTD20 WILD-TYPE 250   3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCTD20 MUTATED      4    1
  KCTD20 WILD-TYPE  250    3
   clus
vv  KCTD20 MUTATED KCTD20 WILD-TYPE
  0              4              250
  1              1                3
[1] 2 2
[1] FALSE
D31V6, binary
                  cls
clus                 0   1
  KCTD20 MUTATED     4   1
  KCTD20 WILD-TYPE 265   3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCTD20 MUTATED      4    1
  KCTD20 WILD-TYPE  265    3
   clus
vv  KCTD20 MUTATED KCTD20 WILD-TYPE
  0              4              265
  1              1                3
[1] 2 2
[1] FALSE
D31V7, binary
                  cls
clus                 0   1
  KCTD20 MUTATED     2   3
  KCTD20 WILD-TYPE 119 249
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCTD20 MUTATED      2    3
  KCTD20 WILD-TYPE  119  249
        clus
vv       KCTD20 MUTATED KCTD20 WILD-TYPE
  FEMALE              2              119
  MALE                3              249
[1] 2 2
[1] FALSE
D31V8, binary
                  cls
clus                 0   1
  KCTD20 MUTATED     4   0
  KCTD20 WILD-TYPE 337   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCTD20 MUTATED      4    0
  KCTD20 WILD-TYPE  337    9
     clus
vv    KCTD20 MUTATED KCTD20 WILD-TYPE
  NO               4              337
  YES              0                9
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  KCTD20 MUTATED                         0                        5
  KCTD20 WILD-TYPE                       3                      358
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  KCTD20 MUTATED                                  0
  KCTD20 WILD-TYPE                                7
D31V9, multiclass
                                  clus
vv                                 KCTD20 MUTATED KCTD20 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                3
  HEPATOCELLULAR CARCINOMA                      5              358
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KCTD20 MUTATED     5   0   0   0
  KCTD20 WILD-TYPE 322  16   1  22
D31V10, multiclass
    clus
vv   KCTD20 MUTATED KCTD20 WILD-TYPE
  R0              5              322
  R1              0               16
  R2              0                1
  RX              0               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KCTD20 MUTATED                                  0     1
  KCTD20 WILD-TYPE                                2   159
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KCTD20 MUTATED                           0     4
  KCTD20 WILD-TYPE                        17   180
D31V11, multiclass
                                  clus
vv                                 KCTD20 MUTATED KCTD20 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         1              159
  BLACK OR AFRICAN AMERICAN                     0               17
  WHITE                                         4              180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V12, binary
                  cls
clus                 0   1
  KCTD20 MUTATED     0   5
  KCTD20 WILD-TYPE  18 332
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCTD20 MUTATED      0    5
  KCTD20 WILD-TYPE   18  332
                        clus
vv                       KCTD20 MUTATED KCTD20 WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              5              332
[1] 2 2
[1] FALSE

Clustering(32) Variable = GPR110 MUTATION ANALYSIS
D32V1, survival
                  sevent
clus2                0   1
  GPR110 MUTATED     3   3
  GPR110 WILD-TYPE 234 127
  GPR110 MUTATED GPR110 WILD-TYPE 
               6              361 
  GPR110 MUTATED GPR110 WILD-TYPE 
               3              127 
$`GPR110 MUTATED`
TCGA-CC-A7IH TCGA-DD-A116 TCGA-DD-A1EE TCGA-DD-AAD6 TCGA-DD-AADB TCGA-ZP-A9CV 
       12.00        53.33        11.47        22.09        40.83        35.77 

$`GPR110 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
       21.34         9.83        13.12        12.56         8.61         9.14 
TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.86         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       79.73        37.78        83.57       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ 
       32.52        21.70        30.97        26.37        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       44.22        40.08        40.54        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
        0.39        29.52        14.89        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       25.08        26.63        25.78        50.33        35.08        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       89.69        82.62        59.93        72.39        80.71        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        60.99 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        9.73         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.39        13.68        51.06        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
       22.95        24.46        20.42        17.10        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       11.87        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CY 
       18.28        33.86        30.41        22.78        13.55        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.21        35.87        25.15        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  GPR110 MUTATED GPR110 WILD-TYPE 
           11.47             0.03 
  GPR110 MUTATED GPR110 WILD-TYPE 
           53.33           120.82 
  GPR110 MUTATED GPR110 WILD-TYPE 
           28.93            19.76 
[1] "11.5 - 53.3 (28.9)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1.3"
D32V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  GPR110 MUTATED         1        0         0          4          0          0
  GPR110 WILD-TYPE     173       86         3         60          9          9
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  GPR110 MUTATED          0         0         0
  GPR110 WILD-TYPE        2         1         2
D32V3, multiclass
            clus
vv           GPR110 MUTATED GPR110 WILD-TYPE
  STAGE I                 1              173
  STAGE II                0               86
  STAGE III               0                3
  STAGE IIIA              4               60
  STAGE IIIB              0                9
  STAGE IIIC              0                9
  STAGE IV                0                2
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR110 MUTATED     2   0   4   0
  GPR110 WILD-TYPE 182  94  75  13
D32V4, multiclass
    clus
vv   GPR110 MUTATED GPR110 WILD-TYPE
  T1              2              182
  T2              0               94
  T3              4               75
  T4              0               13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V5, binary
                  cls
clus                 0   1
  GPR110 MUTATED     5   0
  GPR110 WILD-TYPE 249   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR110 MUTATED      5    0
  GPR110 WILD-TYPE  249    4
   clus
vv  GPR110 MUTATED GPR110 WILD-TYPE
  0              5              249
  1              0                4
[1] 2 2
[1] FALSE
D32V6, binary
                  cls
clus                 0   1
  GPR110 MUTATED     5   0
  GPR110 WILD-TYPE 264   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR110 MUTATED      5    0
  GPR110 WILD-TYPE  264    4
   clus
vv  GPR110 MUTATED GPR110 WILD-TYPE
  0              5              264
  1              0                4
[1] 2 2
[1] FALSE
D32V7, binary
                  cls
clus                 0   1
  GPR110 MUTATED     0   6
  GPR110 WILD-TYPE 121 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR110 MUTATED      0    6
  GPR110 WILD-TYPE  121  246
        clus
vv       GPR110 MUTATED GPR110 WILD-TYPE
  FEMALE              0              121
  MALE                6              246
[1] 2 2
[1] FALSE
D32V8, binary
                  cls
clus                 0   1
  GPR110 MUTATED     5   1
  GPR110 WILD-TYPE 336   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR110 MUTATED      5    1
  GPR110 WILD-TYPE  336    8
     clus
vv    GPR110 MUTATED GPR110 WILD-TYPE
  NO               5              336
  YES              1                8
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  GPR110 MUTATED                         0                        6
  GPR110 WILD-TYPE                       3                      357
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  GPR110 MUTATED                                  0
  GPR110 WILD-TYPE                                7
D32V9, multiclass
                                  clus
vv                                 GPR110 MUTATED GPR110 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                3
  HEPATOCELLULAR CARCINOMA                      6              357
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GPR110 MUTATED     6   0   0   0
  GPR110 WILD-TYPE 321  16   1  22
D32V10, multiclass
    clus
vv   GPR110 MUTATED GPR110 WILD-TYPE
  R0              6              321
  R1              0               16
  R2              0                1
  RX              0               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR110 MUTATED                                  0     4
  GPR110 WILD-TYPE                                2   156
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GPR110 MUTATED                           0     2
  GPR110 WILD-TYPE                        17   182
D32V11, multiclass
                                  clus
vv                                 GPR110 MUTATED GPR110 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         4              156
  BLACK OR AFRICAN AMERICAN                     0               17
  WHITE                                         2              182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V12, binary
                  cls
clus                 0   1
  GPR110 MUTATED     0   6
  GPR110 WILD-TYPE  18 331
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR110 MUTATED      0    6
  GPR110 WILD-TYPE   18  331
                        clus
vv                       GPR110 MUTATED GPR110 WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              6              331
[1] 2 2
[1] FALSE

Clustering(33) Variable = CEP164 MUTATION ANALYSIS
D33V1, survival
                  sevent
clus2                0   1
  CEP164 MUTATED     4   5
  CEP164 WILD-TYPE 233 125
  CEP164 MUTATED CEP164 WILD-TYPE 
               9              358 
  CEP164 MUTATED CEP164 WILD-TYPE 
               5              125 
$`CEP164 MUTATED`
TCGA-DD-A113 TCGA-DD-A119 TCGA-DD-A39Y TCGA-DD-A4NA TCGA-DD-AACA TCGA-DD-AACG 
       79.73         7.33         5.62        33.14        75.65        15.42 
TCGA-FV-A2QR TCGA-G3-A3CJ TCGA-HP-A5N0 
       19.10        19.53        37.71 

$`CEP164 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       21.34         9.83        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
        9.14         9.86         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A 
        8.15        37.78        83.57        53.33       113.00         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.69        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB 
       20.12       102.74       107.11        13.78        30.61        32.52 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       21.70        30.97        26.37        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACH 
       76.41        55.40        12.53        71.80        12.00         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
       53.19        69.11         0.30         3.52        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
       61.68        13.64        14.20        59.31        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       50.33        46.82         5.59        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       40.54        40.83        13.97        40.47        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       37.64        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       29.52        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.21        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
       18.61        19.99         4.64        23.74        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       26.63        25.78        50.33        35.08        90.48        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       82.62        59.93        72.39        80.71        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       64.77        62.47        66.25        65.39        60.99        53.69 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       29.92        26.93        28.08        13.91        13.35         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20        12.82         0.20        14.04        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.35         1.84         0.20        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       19.59         0.62        11.93        14.40        60.89        23.97 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S 
       27.88        12.03         0.03         0.33         0.39        13.68 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       51.06        53.79        28.27        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
        5.92        19.23        25.25        22.95        24.46        20.42 
TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       17.10        14.70        20.78        11.87        14.14        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.65        11.80        12.23        13.55         0.89        11.64 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        28.90         1.02         2.20         2.99 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06        16.83        11.80        27.25        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        26.27        17.69        21.01         3.09 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        15.52        36.10        27.88        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        1.71        15.98        10.75        11.34         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       20.22        24.85        18.28        33.86        30.41        22.78 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       13.55        35.77        25.71        23.21        35.87        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        79.30        11.21 

  CEP164 MUTATED CEP164 WILD-TYPE 
            5.62             0.03 
  CEP164 MUTATED CEP164 WILD-TYPE 
           79.73           120.82 
  CEP164 MUTATED CEP164 WILD-TYPE 
          19.530           19.775 
[1] "5.6 - 79.7 (19.5)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.4"
D33V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CEP164 MUTATED         3        3         0          0          0          1
  CEP164 WILD-TYPE     171       83         3         64          9          8
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  CEP164 MUTATED          1         0         0
  CEP164 WILD-TYPE        1         1         2
D33V3, multiclass
            clus
vv           CEP164 MUTATED CEP164 WILD-TYPE
  STAGE I                 3              171
  STAGE II                3               83
  STAGE III               0                3
  STAGE IIIA              0               64
  STAGE IIIB              0                9
  STAGE IIIC              1                8
  STAGE IV                1                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CEP164 MUTATED     3   4   1   0
  CEP164 WILD-TYPE 181  90  78  13
D33V4, multiclass
    clus
vv   CEP164 MUTATED CEP164 WILD-TYPE
  T1              3              181
  T2              4               90
  T3              1               78
  T4              0               13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V5, binary
                  cls
clus                 0   1
  CEP164 MUTATED     6   1
  CEP164 WILD-TYPE 248   3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP164 MUTATED      6    1
  CEP164 WILD-TYPE  248    3
   clus
vv  CEP164 MUTATED CEP164 WILD-TYPE
  0              6              248
  1              1                3
[1] 2 2
[1] FALSE
D33V6, binary
                  cls
clus                 0   1
  CEP164 MUTATED     8   1
  CEP164 WILD-TYPE 261   3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP164 MUTATED      8    1
  CEP164 WILD-TYPE  261    3
   clus
vv  CEP164 MUTATED CEP164 WILD-TYPE
  0              8              261
  1              1                3
[1] 2 2
[1] FALSE
D33V7, binary
                  cls
clus                 0   1
  CEP164 MUTATED     3   6
  CEP164 WILD-TYPE 118 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP164 MUTATED      3    6
  CEP164 WILD-TYPE  118  246
        clus
vv       CEP164 MUTATED CEP164 WILD-TYPE
  FEMALE              3              118
  MALE                6              246
[1] 2 2
[1] FALSE
D33V8, binary
                  cls
clus                 0   1
  CEP164 MUTATED     8   0
  CEP164 WILD-TYPE 333   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP164 MUTATED      8    0
  CEP164 WILD-TYPE  333    9
     clus
vv    CEP164 MUTATED CEP164 WILD-TYPE
  NO               8              333
  YES              0                9
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  CEP164 MUTATED                         0                        9
  CEP164 WILD-TYPE                       3                      354
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  CEP164 MUTATED                                  0
  CEP164 WILD-TYPE                                7
D33V9, multiclass
                                  clus
vv                                 CEP164 MUTATED CEP164 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                3
  HEPATOCELLULAR CARCINOMA                      9              354
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CEP164 MUTATED     7   0   1   1
  CEP164 WILD-TYPE 320  16   0  21
D33V10, multiclass
    clus
vv   CEP164 MUTATED CEP164 WILD-TYPE
  R0              7              320
  R1              0               16
  R2              1                0
  RX              1               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CEP164 MUTATED                                  1     4
  CEP164 WILD-TYPE                                1   156
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CEP164 MUTATED                           0     3
  CEP164 WILD-TYPE                        17   181
D33V11, multiclass
                                  clus
vv                                 CEP164 MUTATED CEP164 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                1
  ASIAN                                         4              156
  BLACK OR AFRICAN AMERICAN                     0               17
  WHITE                                         3              181
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V12, binary
                  cls
clus                 0   1
  CEP164 MUTATED     0   8
  CEP164 WILD-TYPE  18 329
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP164 MUTATED      0    8
  CEP164 WILD-TYPE   18  329
                        clus
vv                       CEP164 MUTATED CEP164 WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              8              329
[1] 2 2
[1] FALSE

Clustering(34) Variable = TCEAL6 MUTATION ANALYSIS
D34V1, survival
                  sevent
clus2                0   1
  TCEAL6 MUTATED     1   3
  TCEAL6 WILD-TYPE 236 127
  TCEAL6 MUTATED TCEAL6 WILD-TYPE 
               4              363 
  TCEAL6 MUTATED TCEAL6 WILD-TYPE 
               3              127 
$`TCEAL6 MUTATED`
TCGA-DD-A1EG TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-G3-A3CJ 
       45.11         5.62        25.81        19.53 

$`TCEAL6 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       21.34         9.83        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
        9.14         9.86         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.15        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65        11.47        12.95 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       27.19        55.69        19.76         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ 
       32.52        21.70        30.97        26.37        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       34.49        20.91         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
       14.33        66.67        15.58        18.21        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        89.69        82.62        59.93        72.39 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        60.99        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        20.61        19.59         0.62        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 
       14.40        60.89        23.97        19.10        27.88        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.03         0.33         0.39        13.68        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
       28.27        14.86        21.53        25.64         5.92        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       25.25        22.95        24.46        20.42        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       20.78        11.87        14.14        15.78        15.65        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       12.23        13.55         0.89        11.64         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       58.88        26.27        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        22.78        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        25.71        23.21        35.87        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  TCEAL6 MUTATED TCEAL6 WILD-TYPE 
            5.62             0.03 
  TCEAL6 MUTATED TCEAL6 WILD-TYPE 
           45.11           120.82 
  TCEAL6 MUTATED TCEAL6 WILD-TYPE 
           22.67            19.76 
[1] "5.6 - 45.1 (22.7)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "2.3"
D34V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TCEAL6 MUTATED         3        1         0          0          0          0
  TCEAL6 WILD-TYPE     171       85         3         64          9          9
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  TCEAL6 MUTATED          0         0         0
  TCEAL6 WILD-TYPE        2         1         2
D34V3, multiclass
            clus
vv           TCEAL6 MUTATED TCEAL6 WILD-TYPE
  STAGE I                 3              171
  STAGE II                1               85
  STAGE III               0                3
  STAGE IIIA              0               64
  STAGE IIIB              0                9
  STAGE IIIC              0                9
  STAGE IV                0                2
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TCEAL6 MUTATED     3   1   0   0
  TCEAL6 WILD-TYPE 181  93  79  13
D34V4, multiclass
    clus
vv   TCEAL6 MUTATED TCEAL6 WILD-TYPE
  T1              3              181
  T2              1               93
  T3              0               79
  T4              0               13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V5, binary
                  cls
clus                 0   1
  TCEAL6 MUTATED     2   0
  TCEAL6 WILD-TYPE 252   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL6 MUTATED      2    0
  TCEAL6 WILD-TYPE  252    4
   clus
vv  TCEAL6 MUTATED TCEAL6 WILD-TYPE
  0              2              252
  1              0                4
[1] 2 2
[1] FALSE
D34V6, binary
                  cls
clus                 0   1
  TCEAL6 MUTATED     4   0
  TCEAL6 WILD-TYPE 265   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL6 MUTATED      4    0
  TCEAL6 WILD-TYPE  265    4
   clus
vv  TCEAL6 MUTATED TCEAL6 WILD-TYPE
  0              4              265
  1              0                4
[1] 2 2
[1] FALSE
D34V7, binary
                  cls
clus                 0   1
  TCEAL6 MUTATED     0   4
  TCEAL6 WILD-TYPE 121 248
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL6 MUTATED      0    4
  TCEAL6 WILD-TYPE  121  248
        clus
vv       TCEAL6 MUTATED TCEAL6 WILD-TYPE
  FEMALE              0              121
  MALE                4              248
[1] 2 2
[1] FALSE
D34V8, binary
                  cls
clus                 0   1
  TCEAL6 MUTATED     4   0
  TCEAL6 WILD-TYPE 337   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL6 MUTATED      4    0
  TCEAL6 WILD-TYPE  337    9
     clus
vv    TCEAL6 MUTATED TCEAL6 WILD-TYPE
  NO               4              337
  YES              0                9
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  TCEAL6 MUTATED                         0                        4
  TCEAL6 WILD-TYPE                       3                      359
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  TCEAL6 MUTATED                                  0
  TCEAL6 WILD-TYPE                                7
D34V9, multiclass
                                  clus
vv                                 TCEAL6 MUTATED TCEAL6 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                3
  HEPATOCELLULAR CARCINOMA                      4              359
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TCEAL6 MUTATED     4   0   0   0
  TCEAL6 WILD-TYPE 323  16   1  22
D34V10, multiclass
    clus
vv   TCEAL6 MUTATED TCEAL6 WILD-TYPE
  R0              4              323
  R1              0               16
  R2              0                1
  RX              0               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TCEAL6 MUTATED                                  1     1
  TCEAL6 WILD-TYPE                                1   159
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TCEAL6 MUTATED                           0     2
  TCEAL6 WILD-TYPE                        17   182
D34V11, multiclass
                                  clus
vv                                 TCEAL6 MUTATED TCEAL6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                1
  ASIAN                                         1              159
  BLACK OR AFRICAN AMERICAN                     0               17
  WHITE                                         2              182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V12, binary
                  cls
clus                 0   1
  TCEAL6 MUTATED     0   4
  TCEAL6 WILD-TYPE  18 333
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL6 MUTATED      0    4
  TCEAL6 WILD-TYPE   18  333
                        clus
vv                       TCEAL6 MUTATED TCEAL6 WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              4              333
[1] 2 2
[1] FALSE

Clustering(35) Variable = DNAJC28 MUTATION ANALYSIS
D35V1, survival
                   sevent
clus2                 0   1
  DNAJC28 MUTATED     2   2
  DNAJC28 WILD-TYPE 235 128
  DNAJC28 MUTATED DNAJC28 WILD-TYPE 
                4               363 
  DNAJC28 MUTATED DNAJC28 WILD-TYPE 
                2               128 
$`DNAJC28 MUTATED`
TCGA-BC-A112 TCGA-G3-A3CG TCGA-CC-5263 TCGA-FV-A496 
        5.03        22.13         4.24         0.33 

$`DNAJC28 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
        6.38        81.73        30.74        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
        2.14        31.27        12.72        24.56         0.76         7.04 
TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
       10.32        44.02        29.52         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
      120.82        40.41        56.91        49.84        47.74        18.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       20.81        22.92         1.18         8.55        13.02        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 
       10.59         0.66        17.10        14.76         1.51        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.38         1.12        44.42        45.93         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       14.60        18.48        44.81        13.45         0.66         4.24 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A123 
        8.22         2.86         3.19         3.39         3.35         7.20 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.32         9.86         9.96        10.36        11.93        11.41 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
        9.99         8.94         7.13        21.34         9.83        12.00 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT 
       13.12        12.56         8.61         9.14         9.86         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 
       11.31         9.17         6.94         8.15        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65        11.47        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ 
       32.52        21.70        30.97        26.37        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       34.49        20.91         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
       14.33        66.67        15.58        18.21        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        89.69        82.62        59.93        72.39 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        60.99        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        20.61        19.59         0.62        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 
       14.40        60.89        23.97        19.10        27.88        12.03 
TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       25.25        22.95        24.46        20.42        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       20.78        11.87        14.14        15.78        15.65        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       12.23        13.55         0.89        11.64         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       58.88        26.27        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        22.78        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        25.71        23.21        35.87        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  DNAJC28 MUTATED DNAJC28 WILD-TYPE 
             0.33              0.03 
  DNAJC28 MUTATED DNAJC28 WILD-TYPE 
            22.13            120.82 
  DNAJC28 MUTATED DNAJC28 WILD-TYPE 
            4.635            19.790 
[1] "0.3 - 22.1 (4.6)"   "0.0 - 120.8 (19.8)"
[1] "hr=" "4.1"
D35V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DNAJC28 MUTATED         2        0         0          1          0          0
  DNAJC28 WILD-TYPE     172       86         3         63          9          9
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  DNAJC28 MUTATED          0         0         0
  DNAJC28 WILD-TYPE        2         1         2
D35V3, multiclass
            clus
vv           DNAJC28 MUTATED DNAJC28 WILD-TYPE
  STAGE I                  2               172
  STAGE II                 0                86
  STAGE III                0                 3
  STAGE IIIA               1                63
  STAGE IIIB               0                 9
  STAGE IIIC               0                 9
  STAGE IV                 0                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  DNAJC28 MUTATED     2   0   2   0
  DNAJC28 WILD-TYPE 182  94  77  13
D35V4, multiclass
    clus
vv   DNAJC28 MUTATED DNAJC28 WILD-TYPE
  T1               2               182
  T2               0                94
  T3               2                77
  T4               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V5, binary
                   cls
clus                  0   1
  DNAJC28 MUTATED     2   0
  DNAJC28 WILD-TYPE 252   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC28 MUTATED      2    0
  DNAJC28 WILD-TYPE  252    4
   clus
vv  DNAJC28 MUTATED DNAJC28 WILD-TYPE
  0               2               252
  1               0                 4
[1] 2 2
[1] FALSE
D35V6, binary
                   cls
clus                  0   1
  DNAJC28 MUTATED     3   0
  DNAJC28 WILD-TYPE 266   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC28 MUTATED      3    0
  DNAJC28 WILD-TYPE  266    4
   clus
vv  DNAJC28 MUTATED DNAJC28 WILD-TYPE
  0               3               266
  1               0                 4
[1] 2 2
[1] FALSE
D35V7, binary
                   cls
clus                  0   1
  DNAJC28 MUTATED     1   3
  DNAJC28 WILD-TYPE 120 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC28 MUTATED      1    3
  DNAJC28 WILD-TYPE  120  249
        clus
vv       DNAJC28 MUTATED DNAJC28 WILD-TYPE
  FEMALE               1               120
  MALE                 3               249
[1] 2 2
[1] FALSE
D35V8, binary
                   cls
clus                  0   1
  DNAJC28 MUTATED     3   0
  DNAJC28 WILD-TYPE 338   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC28 MUTATED      3    0
  DNAJC28 WILD-TYPE  338    9
     clus
vv    DNAJC28 MUTATED DNAJC28 WILD-TYPE
  NO                3               338
  YES               0                 9
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  DNAJC28 MUTATED                         0                        4
  DNAJC28 WILD-TYPE                       3                      359
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  DNAJC28 MUTATED                                  0
  DNAJC28 WILD-TYPE                                7
D35V9, multiclass
                                  clus
vv                                 DNAJC28 MUTATED DNAJC28 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 3
  HEPATOCELLULAR CARCINOMA                       4               359
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  DNAJC28 MUTATED     2   1   0   1
  DNAJC28 WILD-TYPE 325  15   1  21
D35V10, multiclass
    clus
vv   DNAJC28 MUTATED DNAJC28 WILD-TYPE
  R0               2               325
  R1               1                15
  R2               0                 1
  RX               1                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNAJC28 MUTATED                                  0     1
  DNAJC28 WILD-TYPE                                2   159
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  DNAJC28 MUTATED                           0     3
  DNAJC28 WILD-TYPE                        17   181
D35V11, multiclass
                                  clus
vv                                 DNAJC28 MUTATED DNAJC28 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1               159
  BLACK OR AFRICAN AMERICAN                      0                17
  WHITE                                          3               181
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V12, binary
                   cls
clus                  0   1
  DNAJC28 MUTATED     0   4
  DNAJC28 WILD-TYPE  18 333
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC28 MUTATED      0    4
  DNAJC28 WILD-TYPE   18  333
                        clus
vv                       DNAJC28 MUTATED DNAJC28 WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO               4               333
[1] 2 2
[1] FALSE

Clustering(36) Variable = FOXI1 MUTATION ANALYSIS
D36V1, survival
                 sevent
clus2               0   1
  FOXI1 MUTATED     2   3
  FOXI1 WILD-TYPE 235 127
  FOXI1 MUTATED FOXI1 WILD-TYPE 
              5             362 
  FOXI1 MUTATED FOXI1 WILD-TYPE 
              3             127 
$`FOXI1 MUTATED`
TCGA-CC-5258 TCGA-DD-A1EE TCGA-DD-A3A0 TCGA-DD-AADO TCGA-G3-A3CJ 
        4.24        11.47        25.81        14.89        19.53 

$`FOXI1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.66         8.22         2.86         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.35         7.20         3.32         9.86         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
       11.93        11.41         9.99         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        9.83        12.00        13.12        12.56         8.61         9.14 
TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.86         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       66.31        19.79        75.65        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.69         5.62        19.76         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ 
       32.52        21.70        30.97        26.37        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ 
       34.49        20.91         0.39        29.52        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       66.67        15.58        18.21        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 
       18.15        20.98        18.61        19.99         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       15.72        25.08        26.63        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       90.48        89.69        82.62        59.93        72.39        80.71 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       60.99        53.69        29.92        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         9.73         0.20        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       13.15        13.41        13.35         1.84         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       19.99        20.61        19.59         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI 
       14.86        21.53        25.64         5.92        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
       22.95        24.46        20.42        17.10        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       11.87        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  FOXI1 MUTATED FOXI1 WILD-TYPE 
           4.24            0.03 
  FOXI1 MUTATED FOXI1 WILD-TYPE 
          25.81          120.82 
  FOXI1 MUTATED FOXI1 WILD-TYPE 
          14.89           19.89 
[1] "4.2 - 25.8 (14.9)"  "0.0 - 120.8 (19.9)"
[1] "hr=" "2.6"
D36V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  FOXI1 MUTATED         2        2         0          1          0          0
  FOXI1 WILD-TYPE     172       84         3         63          9          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  FOXI1 MUTATED          0         0         0
  FOXI1 WILD-TYPE        2         1         2
D36V3, multiclass
            clus
vv           FOXI1 MUTATED FOXI1 WILD-TYPE
  STAGE I                2             172
  STAGE II               2              84
  STAGE III              0               3
  STAGE IIIA             1              63
  STAGE IIIB             0               9
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FOXI1 MUTATED     2   2   1   0
  FOXI1 WILD-TYPE 182  92  78  13
D36V4, multiclass
    clus
vv   FOXI1 MUTATED FOXI1 WILD-TYPE
  T1             2             182
  T2             2              92
  T3             1              78
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V5, binary
                 cls
clus                0   1
  FOXI1 MUTATED     4   0
  FOXI1 WILD-TYPE 250   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXI1 MUTATED      4    0
  FOXI1 WILD-TYPE  250    4
   clus
vv  FOXI1 MUTATED FOXI1 WILD-TYPE
  0             4             250
  1             0               4
[1] 2 2
[1] FALSE
D36V6, binary
                 cls
clus                0   1
  FOXI1 MUTATED     5   0
  FOXI1 WILD-TYPE 264   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXI1 MUTATED      5    0
  FOXI1 WILD-TYPE  264    4
   clus
vv  FOXI1 MUTATED FOXI1 WILD-TYPE
  0             5             264
  1             0               4
[1] 2 2
[1] FALSE
D36V7, binary
                 cls
clus                0   1
  FOXI1 MUTATED     0   5
  FOXI1 WILD-TYPE 121 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXI1 MUTATED      0    5
  FOXI1 WILD-TYPE  121  247
        clus
vv       FOXI1 MUTATED FOXI1 WILD-TYPE
  FEMALE             0             121
  MALE               5             247
[1] 2 2
[1] FALSE
D36V8, binary
                 cls
clus                0   1
  FOXI1 MUTATED     5   0
  FOXI1 WILD-TYPE 336   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXI1 MUTATED      5    0
  FOXI1 WILD-TYPE  336    9
     clus
vv    FOXI1 MUTATED FOXI1 WILD-TYPE
  NO              5             336
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  FOXI1 MUTATED                         0                        5
  FOXI1 WILD-TYPE                       3                      358
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  FOXI1 MUTATED                                  0
  FOXI1 WILD-TYPE                                7
D36V9, multiclass
                                  clus
vv                                 FOXI1 MUTATED FOXI1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                     5             358
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FOXI1 MUTATED     4   0   0   1
  FOXI1 WILD-TYPE 323  16   1  21
D36V10, multiclass
    clus
vv   FOXI1 MUTATED FOXI1 WILD-TYPE
  R0             4             323
  R1             0              16
  R2             0               1
  RX             1              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FOXI1 MUTATED                                  1     2
  FOXI1 WILD-TYPE                                1   158
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FOXI1 MUTATED                           0     2
  FOXI1 WILD-TYPE                        17   182
D36V11, multiclass
                                  clus
vv                                 FOXI1 MUTATED FOXI1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               1
  ASIAN                                        2             158
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        2             182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V12, binary
                 cls
clus                0   1
  FOXI1 MUTATED     0   5
  FOXI1 WILD-TYPE  18 332
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXI1 MUTATED      0    5
  FOXI1 WILD-TYPE   18  332
                        clus
vv                       FOXI1 MUTATED FOXI1 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             5             332
[1] 2 2
[1] FALSE

Clustering(37) Variable = KRTAP5-7 MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  KRTAP5-7 MUTATED     3   0
  KRTAP5-7 WILD-TYPE 234 130
  KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE 
                 3                364 
  KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE 
                 0                130 
$`KRTAP5-7 MUTATED`
TCGA-DD-A4NJ TCGA-FV-A495 TCGA-RG-A7D4 
       30.51         0.03        36.10 

$`KRTAP5-7 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       21.34         9.83        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
        9.14         9.86         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.15        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65        11.47        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       45.11        49.15         6.02        33.04        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       21.14        27.19        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF 
       13.78        30.61        33.14        32.52        21.70        30.97 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       26.37        30.15        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        71.80        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       69.11         0.30         3.52        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV 
       13.64        14.20        59.31        51.35        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       46.82         5.59        47.67         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        42.58        44.22        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.83        13.97        40.47        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       35.67        35.05        34.49        20.91         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       14.89        15.06        14.33        66.67        15.58        18.21 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       19.30        18.25        18.25        18.15        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       19.99         4.64        23.74        15.72        25.08        26.63 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       25.78        50.33        35.08        90.48        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       59.93        72.39        80.71        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        60.99        53.69        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       26.93        28.08        13.91        13.35         9.73         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
       12.82         0.20        14.04        13.15        13.41        13.35 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        1.84         0.20        18.74        19.99        20.61        19.59 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        0.62        11.93        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       27.88        12.03         0.33         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       19.53        19.23        25.25        22.95        24.46        20.42 
TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       17.10        14.70        20.78        11.87        14.14        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.65        11.80        12.23        13.55         0.89        11.64 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 
       37.71        17.06        16.83        11.80        27.25        29.79 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       13.97        12.03         9.57        16.67        22.95        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        7.53        10.85        58.88        26.27        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB 
        3.09         0.72         0.49         0.30        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       19.04        15.39        15.52        27.88        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        1.71        15.98        10.75        11.34         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       20.22        24.85        18.28        33.86        30.41        22.78 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       13.55        35.77        25.71        23.21        35.87        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        79.30        11.21 

  KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE 
              0.03               0.20 
  KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE 
             36.10             120.82 
  KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE 
             30.51              19.76 
[1] "0.0 - 36.1 (30.5)"  "0.2 - 120.8 (19.8)"
[1] "hr="     "3300000"
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  KRTAP5-7 MUTATED         0        3         0          0          0
  KRTAP5-7 WILD-TYPE     174       83         3         64          9
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  KRTAP5-7 MUTATED            0        1         0         0
  KRTAP5-7 WILD-TYPE          9        1         1         2
D37V3, multiclass
            clus
vv           KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE
  STAGE I                   0                174
  STAGE II                  3                 83
  STAGE III                 0                  3
  STAGE IIIA                0                 64
  STAGE IIIB                0                  9
  STAGE IIIC                0                  9
  STAGE IV                  1                  1
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KRTAP5-7 MUTATED     0   4   0   0
  KRTAP5-7 WILD-TYPE 184  90  79  13
D37V4, multiclass
    clus
vv   KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE
  T1                0                184
  T2                4                 90
  T3                0                 79
  T4                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V5, binary
                    cls
clus                   0   1
  KRTAP5-7 MUTATED     3   0
  KRTAP5-7 WILD-TYPE 251   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-7 MUTATED      3    0
  KRTAP5-7 WILD-TYPE  251    4
   clus
vv  KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE
  0                3                251
  1                0                  4
[1] 2 2
[1] FALSE
D37V6, binary
                    cls
clus                   0   1
  KRTAP5-7 MUTATED     3   1
  KRTAP5-7 WILD-TYPE 266   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-7 MUTATED      3    1
  KRTAP5-7 WILD-TYPE  266    3
   clus
vv  KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE
  0                3                266
  1                1                  3
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  KRTAP5-7 MUTATED     3   1
  KRTAP5-7 WILD-TYPE 118 251
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-7 MUTATED      3    1
  KRTAP5-7 WILD-TYPE  118  251
        clus
vv       KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE
  FEMALE                3                118
  MALE                  1                251
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                   0   1
  KRTAP5-7 MUTATED     3   0
  KRTAP5-7 WILD-TYPE 338   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-7 MUTATED      3    0
  KRTAP5-7 WILD-TYPE  338    9
     clus
vv    KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE
  NO                 3                338
  YES                0                  9
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  KRTAP5-7 MUTATED                         0                        4
  KRTAP5-7 WILD-TYPE                       3                      359
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  KRTAP5-7 MUTATED                                  0
  KRTAP5-7 WILD-TYPE                                7
D37V9, multiclass
                                  clus
vv                                 KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  3
  HEPATOCELLULAR CARCINOMA                        4                359
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KRTAP5-7 MUTATED     3   0   0   1
  KRTAP5-7 WILD-TYPE 324  16   1  21
D37V10, multiclass
    clus
vv   KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE
  R0                3                324
  R1                0                 16
  R2                0                  1
  RX                1                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRTAP5-7 MUTATED                                  0     0
  KRTAP5-7 WILD-TYPE                                2   160
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KRTAP5-7 MUTATED                           1     3
  KRTAP5-7 WILD-TYPE                        16   181
D37V11, multiclass
                                  clus
vv                                 KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                160
  BLACK OR AFRICAN AMERICAN                       1                 16
  WHITE                                           3                181
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V12, binary
                    cls
clus                   0   1
  KRTAP5-7 MUTATED     1   3
  KRTAP5-7 WILD-TYPE  17 334
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-7 MUTATED      1    3
  KRTAP5-7 WILD-TYPE   17  334
                        clus
vv                       KRTAP5-7 MUTATED KRTAP5-7 WILD-TYPE
  HISPANIC OR LATINO                    1                 17
  NOT HISPANIC OR LATINO                3                334
[1] 2 2
[1] FALSE

Clustering(38) Variable = JAK1 MUTATION ANALYSIS
D38V1, survival
                sevent
clus2              0   1
  JAK1 MUTATED     9   5
  JAK1 WILD-TYPE 228 125
  JAK1 MUTATED JAK1 WILD-TYPE 
            14            353 
  JAK1 MUTATED JAK1 WILD-TYPE 
             5            125 
$`JAK1 MUTATED`
TCGA-DD-AADV TCGA-BD-A3EP TCGA-DD-A119 TCGA-DD-A1EB TCGA-DD-A39Y TCGA-DD-AACD 
       18.87        13.45         7.33        66.31         5.62        12.53 
TCGA-DD-AACY TCGA-DD-AAD5 TCGA-DD-AAVX TCGA-ED-A7XP TCGA-ES-A2HT TCGA-G3-A3CJ 
       47.67        44.22        56.48        13.15        14.40        19.53 
TCGA-LG-A9QD TCGA-ZP-A9CV 
       12.03        35.77 

$`JAK1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AAE7 
       17.98        36.66         0.36        90.28        26.83        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        20.81        22.92         1.18         8.55        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        17.10        14.76         1.51 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BW-A5NO TCGA-CC-5258 
       22.36        14.60        18.48        44.81         0.66         4.24 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
        8.22         2.86         3.19         3.39         4.24         3.35 
TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        7.20         3.32         9.86         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS 
       12.00        13.12        12.56         8.61         9.14         9.86 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B 
       37.78        83.57        53.33       113.00         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED 
       21.76        51.29        90.71        79.40        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       11.47        12.95        45.11        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z 
       18.35        13.64        21.14        27.19        55.69        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE 
      107.11        13.78        30.61        33.14        32.52        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        26.37        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       35.67       114.35        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       76.41        55.40        71.80        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
       53.19        69.11         0.30         3.52        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
       61.68        13.64        14.20        59.31        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       50.33        46.82         5.59         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       21.63        42.58        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.05        34.49        20.91         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        23.74        15.72        25.08        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        90.48        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       72.39        80.71        76.18        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        60.99        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       14.04        13.41        13.35         1.84         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A23B 
       19.99        20.61        19.59         0.62        11.93        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.39        13.68        51.06        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       21.53        25.64         5.92        19.23        25.25        22.95 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       24.46        20.42        17.10        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        0.89        11.64         2.14        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       27.25        29.79        13.97         9.57        16.67        22.95 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         7.53        10.85        58.88        26.27        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 
       21.01         3.09         0.72         0.49         0.30        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       19.33        19.04        15.39        15.52        36.10        27.88 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L 
       19.76        16.44         1.71        15.98        10.75        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD 
        0.99        12.99        20.22        24.85        18.28        33.86 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       30.41        22.78        13.55        25.71        23.21        35.87 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        79.30        11.21 

  JAK1 MUTATED JAK1 WILD-TYPE 
          5.62           0.03 
  JAK1 MUTATED JAK1 WILD-TYPE 
         66.31         120.82 
  JAK1 MUTATED JAK1 WILD-TYPE 
        16.635         19.990 
[1] "5.6 - 66.3 (16.6)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "1.1"
D38V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  JAK1 MUTATED         8        3         0          1          0          0
  JAK1 WILD-TYPE     166       83         3         63          9          9
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  JAK1 MUTATED          1         0         0
  JAK1 WILD-TYPE        1         1         2
D38V3, multiclass
            clus
vv           JAK1 MUTATED JAK1 WILD-TYPE
  STAGE I               8            166
  STAGE II              3             83
  STAGE III             0              3
  STAGE IIIA            1             63
  STAGE IIIB            0              9
  STAGE IIIC            0              9
  STAGE IV              1              1
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  JAK1 MUTATED     9   3   2   0
  JAK1 WILD-TYPE 175  91  77  13
D38V4, multiclass
    clus
vv   JAK1 MUTATED JAK1 WILD-TYPE
  T1            9            175
  T2            3             91
  T3            2             77
  T4            0             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V5, binary
                cls
clus               0   1
  JAK1 MUTATED    11   0
  JAK1 WILD-TYPE 243   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK1 MUTATED     11    0
  JAK1 WILD-TYPE  243    4
   clus
vv  JAK1 MUTATED JAK1 WILD-TYPE
  0           11            243
  1            0              4
[1] 2 2
[1] FALSE
D38V6, binary
                cls
clus               0   1
  JAK1 MUTATED    11   1
  JAK1 WILD-TYPE 258   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK1 MUTATED     11    1
  JAK1 WILD-TYPE  258    3
   clus
vv  JAK1 MUTATED JAK1 WILD-TYPE
  0           11            258
  1            1              3
[1] 2 2
[1] FALSE
D38V7, binary
                cls
clus               0   1
  JAK1 MUTATED     3  11
  JAK1 WILD-TYPE 118 241
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK1 MUTATED      3   11
  JAK1 WILD-TYPE  118  241
        clus
vv       JAK1 MUTATED JAK1 WILD-TYPE
  FEMALE            3            118
  MALE             11            241
[1] 2 2
[1] FALSE
D38V8, binary
                cls
clus               0   1
  JAK1 MUTATED    11   1
  JAK1 WILD-TYPE 330   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK1 MUTATED     11    1
  JAK1 WILD-TYPE  330    8
     clus
vv    JAK1 MUTATED JAK1 WILD-TYPE
  NO            11            330
  YES            1              8
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  JAK1 MUTATED                         0                       14
  JAK1 WILD-TYPE                       3                      349
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  JAK1 MUTATED                                  0
  JAK1 WILD-TYPE                                7
D38V9, multiclass
                                  clus
vv                                 JAK1 MUTATED JAK1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              3
  HEPATOCELLULAR CARCINOMA                   14            349
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  JAK1 MUTATED    13   0   1   0
  JAK1 WILD-TYPE 314  16   0  22
D38V10, multiclass
    clus
vv   JAK1 MUTATED JAK1 WILD-TYPE
  R0           13            314
  R1            0             16
  R2            1              0
  RX            0             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  JAK1 MUTATED                                  1     8
  JAK1 WILD-TYPE                                1   152
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  JAK1 MUTATED                           2     2
  JAK1 WILD-TYPE                        15   182
D38V11, multiclass
                                  clus
vv                                 JAK1 MUTATED JAK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              1
  ASIAN                                       8            152
  BLACK OR AFRICAN AMERICAN                   2             15
  WHITE                                       2            182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V12, binary
                cls
clus               0   1
  JAK1 MUTATED     1  12
  JAK1 WILD-TYPE  17 325
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK1 MUTATED      1   12
  JAK1 WILD-TYPE   17  325
                        clus
vv                       JAK1 MUTATED JAK1 WILD-TYPE
  HISPANIC OR LATINO                1             17
  NOT HISPANIC OR LATINO           12            325
[1] 2 2
[1] FALSE

Clustering(39) Variable = DENND4B MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                 0   1
  DENND4B MUTATED     5   7
  DENND4B WILD-TYPE 232 123
  DENND4B MUTATED DENND4B WILD-TYPE 
               12               355 
  DENND4B MUTATED DENND4B WILD-TYPE 
                7               123 
$`DENND4B MUTATED`
TCGA-4R-AA8I TCGA-ES-A2HS TCGA-G3-A3CG TCGA-BC-A3KF TCGA-BD-A3EP TCGA-DD-A1EL 
        8.61        22.62        22.13         0.26        13.45        13.64 
TCGA-DD-AACF TCGA-DD-AAEH TCGA-EP-A2KA TCGA-EP-A2KB TCGA-FV-A2QR TCGA-WQ-A9G7 
       12.00        25.78        20.61        19.59        19.10         0.99 

$`DENND4B WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        11.74        38.40        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A3R2 
       21.83        18.90        23.64         9.96         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 
       81.73        30.74        22.06         1.84        20.75         2.14 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V 
       31.27        12.72        24.56         0.76         7.04        10.32 
TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT 
       44.02        29.52         0.69        40.80        23.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       63.75        41.79        80.28        24.89        27.88       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 
       40.41        56.91        49.84        47.74        18.25        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH 
       22.92         1.18         8.55        13.02        10.78        10.59 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q 
        0.66        17.10        14.76         1.51        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       10.13        27.52        27.52         2.99        25.32        23.38 
TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO 
        1.12        44.42        45.93        22.36        14.60        18.48 
TCGA-BD-A2L6 TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 
       44.81         0.66         4.24         8.22         2.86         3.19 
TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 
        3.39         4.24         3.35         7.20         3.32         9.86 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE 
        9.96        10.36        11.93        11.41         9.99         8.94 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ 
        7.13        21.34         9.83        12.00        13.12        12.56 
TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
        8.61         9.14         9.86         4.60        11.31         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        6.94         8.15        79.73        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
      113.00         7.33         2.60         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65        11.47 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        33.04        18.35 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       21.14        27.19        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF 
       13.78        30.61        33.14        32.52        21.70        30.97 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       26.37        30.15        30.51        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      114.35        13.48         0.53        11.41        75.65        76.41 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       55.40        12.53        71.80        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       69.11         0.30         3.52        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV 
       13.64        14.20        59.31        51.35        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       46.82         5.59        47.67         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        42.58        44.22        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.83        13.97        40.47        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       35.67        35.05        34.49        20.91         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       14.89        15.06        14.33        66.67        15.58        18.21 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       19.30        18.25        18.25        18.15        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       19.99         4.64        23.74        15.72        25.08        26.63 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        90.48        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.39        80.71        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        60.99        53.69        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       28.08        13.91        13.35         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20        14.04        13.15        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
        0.20        18.74        19.99         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       60.89        23.97        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.39        13.68        51.06        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
       22.95        24.46        20.42        17.10        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       11.87        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       10.75        11.34        12.99        20.22        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        22.78        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.21        35.87        25.15        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  DENND4B MUTATED DENND4B WILD-TYPE 
             0.26              0.03 
  DENND4B MUTATED DENND4B WILD-TYPE 
            25.78            120.82 
  DENND4B MUTATED DENND4B WILD-TYPE 
            16.37             19.99 
[1] "0.3 - 25.8 (16.4)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "2.8"
D39V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DENND4B MUTATED         8        2         0          1          0          0
  DENND4B WILD-TYPE     166       84         3         63          9          9
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  DENND4B MUTATED          0         0         0
  DENND4B WILD-TYPE        2         1         2
D39V3, multiclass
            clus
vv           DENND4B MUTATED DENND4B WILD-TYPE
  STAGE I                  8               166
  STAGE II                 2                84
  STAGE III                0                 3
  STAGE IIIA               1                63
  STAGE IIIB               0                 9
  STAGE IIIC               0                 9
  STAGE IV                 0                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  DENND4B MUTATED     8   2   2   0
  DENND4B WILD-TYPE 176  92  77  13
D39V4, multiclass
    clus
vv   DENND4B MUTATED DENND4B WILD-TYPE
  T1               8               176
  T2               2                92
  T3               2                77
  T4               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V5, binary
                   cls
clus                  0   1
  DENND4B MUTATED     6   0
  DENND4B WILD-TYPE 248   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4B MUTATED      6    0
  DENND4B WILD-TYPE  248    4
   clus
vv  DENND4B MUTATED DENND4B WILD-TYPE
  0               6               248
  1               0                 4
[1] 2 2
[1] FALSE
D39V6, binary
                   cls
clus                  0   1
  DENND4B MUTATED     8   0
  DENND4B WILD-TYPE 261   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4B MUTATED      8    0
  DENND4B WILD-TYPE  261    4
   clus
vv  DENND4B MUTATED DENND4B WILD-TYPE
  0               8               261
  1               0                 4
[1] 2 2
[1] FALSE
D39V7, binary
                   cls
clus                  0   1
  DENND4B MUTATED     5   7
  DENND4B WILD-TYPE 116 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4B MUTATED      5    7
  DENND4B WILD-TYPE  116  245
        clus
vv       DENND4B MUTATED DENND4B WILD-TYPE
  FEMALE               5               116
  MALE                 7               245
[1] 2 2
[1] FALSE
D39V8, binary
                   cls
clus                  0   1
  DENND4B MUTATED    10   0
  DENND4B WILD-TYPE 331   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4B MUTATED     10    0
  DENND4B WILD-TYPE  331    9
     clus
vv    DENND4B MUTATED DENND4B WILD-TYPE
  NO               10               331
  YES               0                 9
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  DENND4B MUTATED                         0                       12
  DENND4B WILD-TYPE                       3                      351
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  DENND4B MUTATED                                  0
  DENND4B WILD-TYPE                                7
D39V9, multiclass
                                  clus
vv                                 DENND4B MUTATED DENND4B WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 3
  HEPATOCELLULAR CARCINOMA                      12               351
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  DENND4B MUTATED    10   1   0   1
  DENND4B WILD-TYPE 317  15   1  21
D39V10, multiclass
    clus
vv   DENND4B MUTATED DENND4B WILD-TYPE
  R0              10               317
  R1               1                15
  R2               0                 1
  RX               1                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DENND4B MUTATED                                  0     2
  DENND4B WILD-TYPE                                2   158
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  DENND4B MUTATED                           2     8
  DENND4B WILD-TYPE                        15   176
D39V11, multiclass
                                  clus
vv                                 DENND4B MUTATED DENND4B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2               158
  BLACK OR AFRICAN AMERICAN                      2                15
  WHITE                                          8               176
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V12, binary
                   cls
clus                  0   1
  DENND4B MUTATED     0  11
  DENND4B WILD-TYPE  18 326
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4B MUTATED      0   11
  DENND4B WILD-TYPE   18  326
                        clus
vv                       DENND4B MUTATED DENND4B WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO              11               326
[1] 2 2
[1] FALSE

Clustering(40) Variable = BRD7 MUTATION ANALYSIS
D40V1, survival
                sevent
clus2              0   1
  BRD7 MUTATED     9   1
  BRD7 WILD-TYPE 228 129
  BRD7 MUTATED BRD7 WILD-TYPE 
            10            357 
  BRD7 MUTATED BRD7 WILD-TYPE 
             1            129 
$`BRD7 MUTATED`
TCGA-DD-A1EH TCGA-DD-A39Z TCGA-DD-AACN TCGA-DD-AAD1 TCGA-DD-AAD5 TCGA-DD-AAE6 
       49.15        19.76        42.81        18.54        44.22         4.64 
TCGA-DD-AAEH TCGA-ED-A8O5 TCGA-G3-A3CH TCGA-G3-AAV3 
       25.78        13.35        25.64        13.55 

$`BRD7 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       21.34         9.83        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
        9.14         9.86         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.15        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65        11.47        12.95 
TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       45.11         6.02        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       27.19        55.69         5.62        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       33.14        32.52        21.70        30.97        26.37        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       23.05        22.78         1.45        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        75.65        76.41        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       71.80        12.00        15.42         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        0.30         3.52        58.16        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD6 
       47.67         5.62         4.50        21.63        42.58        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
        0.39        29.52        14.89        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
       20.98        18.61        19.99        23.74        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       26.63        50.33        35.08        90.48        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       59.93        72.39        80.71        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        60.99        53.69        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       26.93        28.08        13.91        13.35         9.73         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O6 
       12.82         0.20        14.04        13.15        13.41         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        20.61        19.59         0.62 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CI TCGA-G3-A3CJ 
       53.79        28.27        14.86        21.53         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        25.25        22.95        24.46        20.42        17.10 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       14.70        20.78        11.87        14.14        15.78        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       11.80        12.23         0.89        11.64         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       58.88        26.27        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        22.78        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        25.71        23.21        35.87        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  BRD7 MUTATED BRD7 WILD-TYPE 
          4.64           0.03 
  BRD7 MUTATED BRD7 WILD-TYPE 
         49.15         120.82 
  BRD7 MUTATED BRD7 WILD-TYPE 
         22.70          19.76 
[1] "4.6 - 49.1 (22.7)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "3.6"
D40V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  BRD7 MUTATED         5        2         1          2          0          0
  BRD7 WILD-TYPE     169       84         2         62          9          9
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  BRD7 MUTATED          0         0         0
  BRD7 WILD-TYPE        2         1         2
D40V3, multiclass
            clus
vv           BRD7 MUTATED BRD7 WILD-TYPE
  STAGE I               5            169
  STAGE II              2             84
  STAGE III             1              2
  STAGE IIIA            2             62
  STAGE IIIB            0              9
  STAGE IIIC            0              9
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BRD7 MUTATED     5   2   3   0
  BRD7 WILD-TYPE 179  92  76  13
D40V4, multiclass
    clus
vv   BRD7 MUTATED BRD7 WILD-TYPE
  T1            5            179
  T2            2             92
  T3            3             76
  T4            0             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V5, binary
                cls
clus               0   1
  BRD7 MUTATED     9   0
  BRD7 WILD-TYPE 245   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD7 MUTATED      9    0
  BRD7 WILD-TYPE  245    4
   clus
vv  BRD7 MUTATED BRD7 WILD-TYPE
  0            9            245
  1            0              4
[1] 2 2
[1] FALSE
D40V6, binary
                cls
clus               0   1
  BRD7 MUTATED    10   0
  BRD7 WILD-TYPE 259   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD7 MUTATED     10    0
  BRD7 WILD-TYPE  259    4
   clus
vv  BRD7 MUTATED BRD7 WILD-TYPE
  0           10            259
  1            0              4
[1] 2 2
[1] FALSE
D40V7, binary
                cls
clus               0   1
  BRD7 MUTATED     5   5
  BRD7 WILD-TYPE 116 247
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD7 MUTATED      5    5
  BRD7 WILD-TYPE  116  247
        clus
vv       BRD7 MUTATED BRD7 WILD-TYPE
  FEMALE            5            116
  MALE              5            247
[1] 2 2
[1] FALSE
D40V8, binary
                cls
clus               0   1
  BRD7 MUTATED     9   0
  BRD7 WILD-TYPE 332   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD7 MUTATED      9    0
  BRD7 WILD-TYPE  332    9
     clus
vv    BRD7 MUTATED BRD7 WILD-TYPE
  NO             9            332
  YES            0              9
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  BRD7 MUTATED                         0                       10
  BRD7 WILD-TYPE                       3                      353
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  BRD7 MUTATED                                  0
  BRD7 WILD-TYPE                                7
D40V9, multiclass
                                  clus
vv                                 BRD7 MUTATED BRD7 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              3
  HEPATOCELLULAR CARCINOMA                   10            353
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BRD7 MUTATED     9   1   0   0
  BRD7 WILD-TYPE 318  15   1  22
D40V10, multiclass
    clus
vv   BRD7 MUTATED BRD7 WILD-TYPE
  R0            9            318
  R1            1             15
  R2            0              1
  RX            0             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRD7 MUTATED                                  0     7
  BRD7 WILD-TYPE                                2   153
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BRD7 MUTATED                           0     2
  BRD7 WILD-TYPE                        17   182
D40V11, multiclass
                                  clus
vv                                 BRD7 MUTATED BRD7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       7            153
  BLACK OR AFRICAN AMERICAN                   0             17
  WHITE                                       2            182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V12, binary
                cls
clus               0   1
  BRD7 MUTATED     0   9
  BRD7 WILD-TYPE  18 328
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD7 MUTATED      0    9
  BRD7 WILD-TYPE   18  328
                        clus
vv                       BRD7 MUTATED BRD7 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            9            328
[1] 2 2
[1] FALSE

Clustering(41) Variable = IDH1 MUTATION ANALYSIS
D41V1, survival
                sevent
clus2              0   1
  IDH1 MUTATED     4   4
  IDH1 WILD-TYPE 233 126
  IDH1 MUTATED IDH1 WILD-TYPE 
             8            359 
  IDH1 MUTATED IDH1 WILD-TYPE 
             4            126 
$`IDH1 MUTATED`
TCGA-BC-A10Q TCGA-CC-5260 TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A4NA TCGA-DD-AADL 
       37.32         2.86        11.47        45.11        33.14        20.91 
TCGA-DD-AAVV TCGA-UB-AA0U 
       80.71        10.75 

$`IDH1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
        1.51        27.91        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        14.60        18.48        44.81        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
        4.24         8.22         3.19         3.39         4.24         3.35 
TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        7.20         3.32         9.86         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS 
       12.00        13.12        12.56         8.61         9.14         9.86 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.79        75.65        12.95        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       18.35        13.64        21.14        27.19        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NB TCGA-DD-A4NE 
      102.74       107.11        13.78        30.61        32.52        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        26.37        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       35.67       114.35        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       76.41        55.40        12.53        71.80        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       42.81        61.68        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADM 
        3.78        37.64        35.67        35.05        34.49         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       29.52        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.21        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
       18.61        19.99         4.64        23.74        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       26.63        25.78        50.33        35.08        90.48        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       82.62        59.93        72.39        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        60.99        53.69        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       26.93        28.08        13.91        13.35         9.73         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
       12.82         0.20        14.04        13.15        13.41        13.35 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        1.84         0.20        18.74        19.99        20.61        19.59 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        0.62        11.93        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S 
       27.88        12.03         0.03         0.33         0.39        13.68 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       51.06        53.79        28.27        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
        5.92        19.53        19.23        25.25        22.95        24.46 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       20.42        17.10        14.70        20.78        11.87        14.14 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       15.78        15.65        11.80        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       11.64         2.14        11.87        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 
        2.99        37.71        17.06        16.83        11.80        27.25 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       29.79        13.97        12.03         9.57        16.67        22.95 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         7.53        10.85        58.88        26.27        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 
       21.01         3.09         0.72         0.49         0.30        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       19.33        19.04        15.39        15.52        36.10        27.88 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-WJ-A86L TCGA-WQ-A9G7 
       19.76        16.44         1.71        15.98        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE 
       12.99        20.22        24.85        18.28        33.86        30.41 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       22.78        13.55        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        79.30        11.21 

  IDH1 MUTATED IDH1 WILD-TYPE 
          2.86           0.03 
  IDH1 MUTATED IDH1 WILD-TYPE 
         80.71         120.82 
  IDH1 MUTATED IDH1 WILD-TYPE 
        27.025         19.760 
[1] "2.9 - 80.7 (27.0)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.4"
D41V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  IDH1 MUTATED         2        2         0          1          0          2
  IDH1 WILD-TYPE     172       84         3         63          9          7
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  IDH1 MUTATED          0         0         0
  IDH1 WILD-TYPE        2         1         2
D41V3, multiclass
            clus
vv           IDH1 MUTATED IDH1 WILD-TYPE
  STAGE I               2            172
  STAGE II              2             84
  STAGE III             0              3
  STAGE IIIA            1             63
  STAGE IIIB            0              9
  STAGE IIIC            2              7
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IDH1 MUTATED     2   4   1   1
  IDH1 WILD-TYPE 182  90  78  12
D41V4, multiclass
    clus
vv   IDH1 MUTATED IDH1 WILD-TYPE
  T1            2            182
  T2            4             90
  T3            1             78
  T4            1             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V5, binary
                cls
clus               0   1
  IDH1 MUTATED     5   1
  IDH1 WILD-TYPE 249   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      5    1
  IDH1 WILD-TYPE  249    3
   clus
vv  IDH1 MUTATED IDH1 WILD-TYPE
  0            5            249
  1            1              3
[1] 2 2
[1] FALSE
D41V6, binary
                cls
clus               0   1
  IDH1 MUTATED     6   0
  IDH1 WILD-TYPE 263   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      6    0
  IDH1 WILD-TYPE  263    4
   clus
vv  IDH1 MUTATED IDH1 WILD-TYPE
  0            6            263
  1            0              4
[1] 2 2
[1] FALSE
D41V7, binary
                cls
clus               0   1
  IDH1 MUTATED     3   5
  IDH1 WILD-TYPE 118 247
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      3    5
  IDH1 WILD-TYPE  118  247
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  FEMALE            3            118
  MALE              5            247
[1] 2 2
[1] FALSE
D41V8, binary
                cls
clus               0   1
  IDH1 MUTATED     8   0
  IDH1 WILD-TYPE 333   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      8    0
  IDH1 WILD-TYPE  333    9
     clus
vv    IDH1 MUTATED IDH1 WILD-TYPE
  NO             8            333
  YES            0              9
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  IDH1 MUTATED                         0                        8
  IDH1 WILD-TYPE                       3                      355
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  IDH1 MUTATED                                  0
  IDH1 WILD-TYPE                                7
D41V9, multiclass
                                  clus
vv                                 IDH1 MUTATED IDH1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              3
  HEPATOCELLULAR CARCINOMA                    8            355
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  IDH1 MUTATED     5   2   0   1
  IDH1 WILD-TYPE 322  14   1  21
D41V10, multiclass
    clus
vv   IDH1 MUTATED IDH1 WILD-TYPE
  R0            5            322
  R1            2             14
  R2            0              1
  RX            1             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IDH1 MUTATED                                  0     3
  IDH1 WILD-TYPE                                2   157
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IDH1 MUTATED                           0     5
  IDH1 WILD-TYPE                        17   179
D41V11, multiclass
                                  clus
vv                                 IDH1 MUTATED IDH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       3            157
  BLACK OR AFRICAN AMERICAN                   0             17
  WHITE                                       5            179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V12, binary
                cls
clus               0   1
  IDH1 MUTATED     0   8
  IDH1 WILD-TYPE  18 329
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      0    8
  IDH1 WILD-TYPE   18  329
                        clus
vv                       IDH1 MUTATED IDH1 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            8            329
[1] 2 2
[1] FALSE

Clustering(42) Variable = CNGA3 MUTATION ANALYSIS
D42V1, survival
                 sevent
clus2               0   1
  CNGA3 MUTATED     6   5
  CNGA3 WILD-TYPE 231 125
  CNGA3 MUTATED CNGA3 WILD-TYPE 
             11             356 
  CNGA3 MUTATED CNGA3 WILD-TYPE 
              5             125 
$`CNGA3 MUTATED`
TCGA-DD-AAE8 TCGA-CC-A7IG TCGA-CC-A7IJ TCGA-DD-A4NE TCGA-DD-AAC8 TCGA-DD-AACJ 
       21.83         9.83        12.56        21.70         0.53        69.11 
TCGA-DD-AADG TCGA-G3-AAV4 TCGA-KR-A7K2 TCGA-UB-A7MB TCGA-ZS-A9CD 
       37.64         0.89        27.25        19.76        45.57 

$`CNGA3 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.17        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        20.81        22.92         1.18         8.55        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        17.10        14.76         1.51 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        14.60        18.48        44.81        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.24         8.22         2.86         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.35         7.20         3.32         9.86         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
       11.93        11.41         9.99         8.94         7.13        21.34 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT 
       12.00        13.12         8.61         9.14         9.86         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 
       11.31         9.17         6.94         8.15        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65        11.47        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       32.52        30.97        26.37        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA 
        1.45        35.67       114.35        13.48        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       76.41        55.40        12.53        71.80        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
        6.41        53.19         0.30         3.52        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
       61.68        13.64        14.20        59.31        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       50.33        46.82         5.59        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       40.54        40.83        13.97        40.47        39.52         3.78 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       35.67        35.05        34.49        20.91         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       14.89        15.06        14.33        66.67        15.58        18.21 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       19.30        18.25        18.25        18.15        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       19.99         4.64        23.74        15.72        25.08        26.63 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       25.78        50.33        35.08        90.48        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       59.93        72.39        80.71        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        60.99        53.69        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       26.93        28.08        13.91        13.35         9.73         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
       12.82         0.20        14.04        13.15        13.41        13.35 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        1.84         0.20        18.74        19.99        20.61        19.59 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        0.62        11.93        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S 
       27.88        12.03         0.03         0.33         0.39        13.68 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       51.06        53.79        28.27        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
        5.92        19.53        19.23        25.25        22.95        24.46 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       20.42        17.10        14.70        20.78        11.87        14.14 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV5 
       15.78        15.65        11.80        12.23        13.55        11.64 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QC 
       37.71        17.06        16.83        11.80        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        26.27        17.69        21.01         3.09 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD 
       15.39        15.52        36.10        27.88        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        22.78        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        25.71        23.21        35.87        25.15        12.99 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  CNGA3 MUTATED CNGA3 WILD-TYPE 
           0.53            0.03 
  CNGA3 MUTATED CNGA3 WILD-TYPE 
          69.11          120.82 
  CNGA3 MUTATED CNGA3 WILD-TYPE 
         21.700          19.675 
[1] "0.5 - 69.1 (21.7)"  "0.0 - 120.8 (19.7)"
[1] "hr=" "1.5"
D42V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CNGA3 MUTATED         4        5         0          2          0          0
  CNGA3 WILD-TYPE     170       81         3         62          9          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  CNGA3 MUTATED          0         0         0
  CNGA3 WILD-TYPE        2         1         2
D42V3, multiclass
            clus
vv           CNGA3 MUTATED CNGA3 WILD-TYPE
  STAGE I                4             170
  STAGE II               5              81
  STAGE III              0               3
  STAGE IIIA             2              62
  STAGE IIIB             0               9
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CNGA3 MUTATED     4   5   2   0
  CNGA3 WILD-TYPE 180  89  77  13
D42V4, multiclass
    clus
vv   CNGA3 MUTATED CNGA3 WILD-TYPE
  T1             4             180
  T2             5              89
  T3             2              77
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V5, binary
                 cls
clus                0   1
  CNGA3 MUTATED     9   0
  CNGA3 WILD-TYPE 245   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNGA3 MUTATED      9    0
  CNGA3 WILD-TYPE  245    4
   clus
vv  CNGA3 MUTATED CNGA3 WILD-TYPE
  0             9             245
  1             0               4
[1] 2 2
[1] FALSE
D42V6, binary
                 cls
clus                0   1
  CNGA3 MUTATED     9   0
  CNGA3 WILD-TYPE 260   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNGA3 MUTATED      9    0
  CNGA3 WILD-TYPE  260    4
   clus
vv  CNGA3 MUTATED CNGA3 WILD-TYPE
  0             9             260
  1             0               4
[1] 2 2
[1] FALSE
D42V7, binary
                 cls
clus                0   1
  CNGA3 MUTATED     2   9
  CNGA3 WILD-TYPE 119 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNGA3 MUTATED      2    9
  CNGA3 WILD-TYPE  119  243
        clus
vv       CNGA3 MUTATED CNGA3 WILD-TYPE
  FEMALE             2             119
  MALE               9             243
[1] 2 2
[1] FALSE
D42V8, binary
                 cls
clus                0   1
  CNGA3 MUTATED    11   0
  CNGA3 WILD-TYPE 330   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNGA3 MUTATED     11    0
  CNGA3 WILD-TYPE  330    9
     clus
vv    CNGA3 MUTATED CNGA3 WILD-TYPE
  NO             11             330
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  CNGA3 MUTATED                         0                       10
  CNGA3 WILD-TYPE                       3                      353
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  CNGA3 MUTATED                                  1
  CNGA3 WILD-TYPE                                6
D42V9, multiclass
                                  clus
vv                                 CNGA3 MUTATED CNGA3 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                    10             353
  HEPATOCHOLANGIOCARCINOMA (MIXED)             1               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CNGA3 MUTATED    11   0   0   0
  CNGA3 WILD-TYPE 316  16   1  22
D42V10, multiclass
    clus
vv   CNGA3 MUTATED CNGA3 WILD-TYPE
  R0            11             316
  R1             0              16
  R2             0               1
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CNGA3 MUTATED                                  0     6
  CNGA3 WILD-TYPE                                2   154
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CNGA3 MUTATED                           0     5
  CNGA3 WILD-TYPE                        17   179
D42V11, multiclass
                                  clus
vv                                 CNGA3 MUTATED CNGA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        6             154
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        5             179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V12, binary
                 cls
clus                0   1
  CNGA3 MUTATED     1   9
  CNGA3 WILD-TYPE  17 328
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNGA3 MUTATED      1    9
  CNGA3 WILD-TYPE   17  328
                        clus
vv                       CNGA3 MUTATED CNGA3 WILD-TYPE
  HISPANIC OR LATINO                 1              17
  NOT HISPANIC OR LATINO             9             328
[1] 2 2
[1] FALSE

Clustering(43) Variable = PLA2G3 MUTATION ANALYSIS
D43V1, survival
                  sevent
clus2                0   1
  PLA2G3 MUTATED     2   4
  PLA2G3 WILD-TYPE 235 126
  PLA2G3 MUTATED PLA2G3 WILD-TYPE 
               6              361 
  PLA2G3 MUTATED PLA2G3 WILD-TYPE 
               4              126 
$`PLA2G3 MUTATED`
TCGA-BC-A217 TCGA-BC-A3KF TCGA-CC-A7IH TCGA-DD-A114 TCGA-DD-A1EE TCGA-DD-AAC8 
       45.93         0.26        12.00        37.78        11.47         0.53 

$`PLA2G3 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A3KG 
        2.99        25.32        23.38         1.12        44.42        22.36 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       14.60        18.48        44.81        13.45         0.66         4.24 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
        8.22         2.86         3.19         3.39         4.24         3.35 
TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        7.20         3.32         9.86         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT 
       13.12        12.56         8.61         9.14         9.86         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A115 
       11.31         9.17         6.94         8.15        79.73        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.33       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        33.04        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       13.64        21.14        27.19        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE 
      107.11        13.78        30.61        33.14        32.52        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        26.37        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
       35.67       114.35        13.48        11.41        75.65        76.41 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        71.80        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
       53.19        69.11         0.30         3.52        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
       61.68        13.64        14.20        59.31        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       50.33        46.82         5.59        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       40.54        40.83        13.97        40.47        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       37.64        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       29.52        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.21        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
       18.61        19.99         4.64        23.74        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       26.63        25.78        50.33        35.08        90.48        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       82.62        59.93        72.39        80.71        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       64.77        62.47        66.25        65.39        60.99        53.69 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       29.92        26.93        28.08        13.91        13.35         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20        12.82         0.20        14.04        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.35         1.84         0.20        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       19.59         0.62        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
       19.10        27.88        12.03         0.03         0.33         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z 
       13.68        51.06        53.79        28.27        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        25.25        22.95 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       24.46        20.42        17.10        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        0.89        11.64         2.14        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       27.25        29.79        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       22.95        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       17.69        21.01         3.09         0.72         0.49         0.30 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.04        19.33        19.04        15.39        15.52        36.10 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       27.88        19.76        16.44         1.71        15.98        10.75 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       11.34         0.99        12.99        20.22        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        22.78        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.21        35.87        25.15        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  PLA2G3 MUTATED PLA2G3 WILD-TYPE 
            0.26             0.03 
  PLA2G3 MUTATED PLA2G3 WILD-TYPE 
           45.93           120.82 
  PLA2G3 MUTATED PLA2G3 WILD-TYPE 
          11.735           19.790 
[1] "0.3 - 45.9 (11.7)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "2.8"
D43V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PLA2G3 MUTATED         2        2         0          2          0          0
  PLA2G3 WILD-TYPE     172       84         3         62          9          9
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  PLA2G3 MUTATED          0         0         0
  PLA2G3 WILD-TYPE        2         1         2
D43V3, multiclass
            clus
vv           PLA2G3 MUTATED PLA2G3 WILD-TYPE
  STAGE I                 2              172
  STAGE II                2               84
  STAGE III               0                3
  STAGE IIIA              2               62
  STAGE IIIB              0                9
  STAGE IIIC              0                9
  STAGE IV                0                2
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PLA2G3 MUTATED     2   2   2   0
  PLA2G3 WILD-TYPE 182  92  77  13
D43V4, multiclass
    clus
vv   PLA2G3 MUTATED PLA2G3 WILD-TYPE
  T1              2              182
  T2              2               92
  T3              2               77
  T4              0               13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V5, binary
                  cls
clus                 0   1
  PLA2G3 MUTATED     3   0
  PLA2G3 WILD-TYPE 251   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLA2G3 MUTATED      3    0
  PLA2G3 WILD-TYPE  251    4
   clus
vv  PLA2G3 MUTATED PLA2G3 WILD-TYPE
  0              3              251
  1              0                4
[1] 2 2
[1] FALSE
D43V6, binary
                  cls
clus                 0   1
  PLA2G3 MUTATED     6   0
  PLA2G3 WILD-TYPE 263   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLA2G3 MUTATED      6    0
  PLA2G3 WILD-TYPE  263    4
   clus
vv  PLA2G3 MUTATED PLA2G3 WILD-TYPE
  0              6              263
  1              0                4
[1] 2 2
[1] FALSE
D43V7, binary
                  cls
clus                 0   1
  PLA2G3 MUTATED     2   4
  PLA2G3 WILD-TYPE 119 248
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLA2G3 MUTATED      2    4
  PLA2G3 WILD-TYPE  119  248
        clus
vv       PLA2G3 MUTATED PLA2G3 WILD-TYPE
  FEMALE              2              119
  MALE                4              248
[1] 2 2
[1] FALSE
D43V8, binary
                  cls
clus                 0   1
  PLA2G3 MUTATED     5   0
  PLA2G3 WILD-TYPE 336   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLA2G3 MUTATED      5    0
  PLA2G3 WILD-TYPE  336    9
     clus
vv    PLA2G3 MUTATED PLA2G3 WILD-TYPE
  NO               5              336
  YES              0                9
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  PLA2G3 MUTATED                         0                        6
  PLA2G3 WILD-TYPE                       3                      357
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  PLA2G3 MUTATED                                  0
  PLA2G3 WILD-TYPE                                7
D43V9, multiclass
                                  clus
vv                                 PLA2G3 MUTATED PLA2G3 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                3
  HEPATOCELLULAR CARCINOMA                      6              357
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PLA2G3 MUTATED     6   0   0   0
  PLA2G3 WILD-TYPE 321  16   1  22
D43V10, multiclass
    clus
vv   PLA2G3 MUTATED PLA2G3 WILD-TYPE
  R0              6              321
  R1              0               16
  R2              0                1
  RX              0               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLA2G3 MUTATED                                  0     2
  PLA2G3 WILD-TYPE                                2   158
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PLA2G3 MUTATED                           1     3
  PLA2G3 WILD-TYPE                        16   181
D43V11, multiclass
                                  clus
vv                                 PLA2G3 MUTATED PLA2G3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         2              158
  BLACK OR AFRICAN AMERICAN                     1               16
  WHITE                                         3              181
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V12, binary
                  cls
clus                 0   1
  PLA2G3 MUTATED     0   4
  PLA2G3 WILD-TYPE  18 333
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLA2G3 MUTATED      0    4
  PLA2G3 WILD-TYPE   18  333
                        clus
vv                       PLA2G3 MUTATED PLA2G3 WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              4              333
[1] 2 2
[1] FALSE

Clustering(44) Variable = HLA-DPB1 MUTATION ANALYSIS
D44V1, survival
                    sevent
clus2                  0   1
  HLA-DPB1 MUTATED     4   1
  HLA-DPB1 WILD-TYPE 233 129
  HLA-DPB1 MUTATED HLA-DPB1 WILD-TYPE 
                 5                362 
  HLA-DPB1 MUTATED HLA-DPB1 WILD-TYPE 
                 1                129 
$`HLA-DPB1 MUTATED`
TCGA-CC-5259 TCGA-DD-A11A TCGA-DD-A1EA TCGA-DD-AACH TCGA-G3-A7M5 
        8.22         2.60        79.40         6.41        14.70 

$`HLA-DPB1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.66         4.24         2.86         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.35         7.20         3.32         9.86         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
       11.93        11.41         9.99         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        9.83        12.00        13.12        12.56         8.61         9.14 
TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.86         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        21.76        51.29        90.71        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65        11.47        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ 
       32.52        21.70        30.97        26.37        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       12.00        15.42        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        40.08        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        29.52        14.89        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       66.67        15.58        18.21        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 
       18.15        20.98        18.61        19.99         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       15.72        25.08        26.63        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       90.48        89.69        82.62        59.93        72.39        80.71 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       60.99        53.69        29.92        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         9.73         0.20        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       13.15        13.41        13.35         1.84         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       19.99        20.61        19.59         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M6 
       25.25        22.95        24.46        20.42        17.10        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       11.87        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  HLA-DPB1 MUTATED HLA-DPB1 WILD-TYPE 
              2.60               0.03 
  HLA-DPB1 MUTATED HLA-DPB1 WILD-TYPE 
             79.40             120.82 
  HLA-DPB1 MUTATED HLA-DPB1 WILD-TYPE 
              8.22              19.89 
[1] "2.6 - 79.4 (8.2)"   "0.0 - 120.8 (19.9)"
[1] "hr=" "1.3"
D44V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  HLA-DPB1 MUTATED         2        2         0          0          0
  HLA-DPB1 WILD-TYPE     172       84         3         64          9
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  HLA-DPB1 MUTATED            1        0         0         0
  HLA-DPB1 WILD-TYPE          8        2         1         2
D44V3, multiclass
            clus
vv           HLA-DPB1 MUTATED HLA-DPB1 WILD-TYPE
  STAGE I                   2                172
  STAGE II                  2                 84
  STAGE III                 0                  3
  STAGE IIIA                0                 64
  STAGE IIIB                0                  9
  STAGE IIIC                1                  8
  STAGE IV                  0                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  HLA-DPB1 MUTATED     2   2   0   1
  HLA-DPB1 WILD-TYPE 182  92  79  12
D44V4, multiclass
    clus
vv   HLA-DPB1 MUTATED HLA-DPB1 WILD-TYPE
  T1                2                182
  T2                2                 92
  T3                0                 79
  T4                1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V5, binary
                    cls
clus                   0   1
  HLA-DPB1 MUTATED     4   0
  HLA-DPB1 WILD-TYPE 250   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HLA-DPB1 MUTATED      4    0
  HLA-DPB1 WILD-TYPE  250    4
   clus
vv  HLA-DPB1 MUTATED HLA-DPB1 WILD-TYPE
  0                4                250
  1                0                  4
[1] 2 2
[1] FALSE
D44V6, binary
                    cls
clus                   0   1
  HLA-DPB1 MUTATED     4   0
  HLA-DPB1 WILD-TYPE 265   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HLA-DPB1 MUTATED      4    0
  HLA-DPB1 WILD-TYPE  265    4
   clus
vv  HLA-DPB1 MUTATED HLA-DPB1 WILD-TYPE
  0                4                265
  1                0                  4
[1] 2 2
[1] FALSE
D44V7, binary
                    cls
clus                   0   1
  HLA-DPB1 MUTATED     1   4
  HLA-DPB1 WILD-TYPE 120 248
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HLA-DPB1 MUTATED      1    4
  HLA-DPB1 WILD-TYPE  120  248
        clus
vv       HLA-DPB1 MUTATED HLA-DPB1 WILD-TYPE
  FEMALE                1                120
  MALE                  4                248
[1] 2 2
[1] FALSE
D44V8, binary
                    cls
clus                   0   1
  HLA-DPB1 MUTATED     4   0
  HLA-DPB1 WILD-TYPE 337   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HLA-DPB1 MUTATED      4    0
  HLA-DPB1 WILD-TYPE  337    9
     clus
vv    HLA-DPB1 MUTATED HLA-DPB1 WILD-TYPE
  NO                 4                337
  YES                0                  9
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  HLA-DPB1 MUTATED                         0                        5
  HLA-DPB1 WILD-TYPE                       3                      358
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  HLA-DPB1 MUTATED                                  0
  HLA-DPB1 WILD-TYPE                                7
D44V9, multiclass
                                  clus
vv                                 HLA-DPB1 MUTATED HLA-DPB1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  3
  HEPATOCELLULAR CARCINOMA                        5                358
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  HLA-DPB1 MUTATED     5   0   0   0
  HLA-DPB1 WILD-TYPE 322  16   1  22
D44V10, multiclass
    clus
vv   HLA-DPB1 MUTATED HLA-DPB1 WILD-TYPE
  R0                5                322
  R1                0                 16
  R2                0                  1
  RX                0                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HLA-DPB1 MUTATED                                  0     4
  HLA-DPB1 WILD-TYPE                                2   156
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  HLA-DPB1 MUTATED                           1     0
  HLA-DPB1 WILD-TYPE                        16   184
D44V11, multiclass
                                  clus
vv                                 HLA-DPB1 MUTATED HLA-DPB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           4                156
  BLACK OR AFRICAN AMERICAN                       1                 16
  WHITE                                           0                184
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V12, binary
                    cls
clus                   0   1
  HLA-DPB1 MUTATED     0   5
  HLA-DPB1 WILD-TYPE  18 332
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HLA-DPB1 MUTATED      0    5
  HLA-DPB1 WILD-TYPE   18  332
                        clus
vv                       HLA-DPB1 MUTATED HLA-DPB1 WILD-TYPE
  HISPANIC OR LATINO                    0                 18
  NOT HISPANIC OR LATINO                5                332
[1] 2 2
[1] FALSE

Clustering(45) Variable = ALMS1 MUTATION ANALYSIS
D45V1, survival
                 sevent
clus2               0   1
  ALMS1 MUTATED    13  11
  ALMS1 WILD-TYPE 224 119
  ALMS1 MUTATED ALMS1 WILD-TYPE 
             24             343 
  ALMS1 MUTATED ALMS1 WILD-TYPE 
             11             119 
$`ALMS1 MUTATED`
TCGA-4R-AA8I TCGA-DD-AAEG TCGA-UB-AA0V TCGA-2Y-A9GY TCGA-5R-AA1C TCGA-BC-A10U 
        8.61        23.64        10.32        24.89        17.10        27.52 
TCGA-CC-A5UD TCGA-DD-A114 TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A7 TCGA-DD-A4NO 
        9.99        37.78        19.76        25.81        13.78        73.81 
TCGA-DD-A73B TCGA-DD-A73F TCGA-DD-AAC9 TCGA-DD-AACI TCGA-DD-AACV TCGA-DD-AACX 
        9.30        35.67        11.41        53.19        50.33         5.59 
TCGA-DD-AACZ TCGA-DD-AADO TCGA-DD-AAVW TCGA-EP-A2KB TCGA-ZP-A9CZ TCGA-ZS-A9CG 
        5.62        14.89        76.18        19.59        23.21        11.21 

$`ALMS1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        11.74        38.40        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 
       21.83        18.90         9.96        22.62         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
       81.73        30.74        22.13        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
        2.14        31.27        12.72        24.56         0.76         7.04 
TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT 
       44.02        29.52         0.69        40.80        23.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       63.75        41.79        80.28        27.88       120.82        40.41 
TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 
       56.91        49.84        47.74        18.25        20.81        22.92 
TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD 
        1.18         8.55        13.02        10.78        10.59         0.66 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T 
       14.76         1.51        27.91        37.32        10.13        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
       10.36        11.93        11.41         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        9.83        12.00        13.12        12.56         8.61         9.14 
TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.86         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       79.73        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       55.69         5.62         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE 
      102.74       107.11        30.61        33.14        32.52        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        26.37        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73G TCGA-DD-AA3A 
       23.93        23.05        22.78         1.45       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
        0.53        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       12.00        15.42         6.41        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 
       51.35        51.52        46.82        47.67         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        42.58        44.22        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.83        13.97        40.47        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       35.67        35.05        34.49        20.91         0.39        29.52 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        23.74        15.72        25.08        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        90.48        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       72.39        80.71        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        60.99        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        19.99        20.61         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       25.25        22.95        24.46        20.42        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       20.78        11.87        14.14        15.78        15.65        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       12.23        13.55         0.89        11.64         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       58.88        26.27        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        22.78        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       35.77        25.71        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF 
       79.30 

  ALMS1 MUTATED ALMS1 WILD-TYPE 
           5.59            0.03 
  ALMS1 MUTATED ALMS1 WILD-TYPE 
          76.18          120.82 
  ALMS1 MUTATED ALMS1 WILD-TYPE 
         19.675          19.790 
[1] "5.6 - 76.2 (19.7)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.4"
D45V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ALMS1 MUTATED        12        8         0          1          1          0
  ALMS1 WILD-TYPE     162       78         3         63          8          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  ALMS1 MUTATED          0         0         0
  ALMS1 WILD-TYPE        2         1         2
D45V3, multiclass
            clus
vv           ALMS1 MUTATED ALMS1 WILD-TYPE
  STAGE I               12             162
  STAGE II               8              78
  STAGE III              0               3
  STAGE IIIA             1              63
  STAGE IIIB             1               8
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ALMS1 MUTATED    12   9   2   0
  ALMS1 WILD-TYPE 172  85  77  13
D45V4, multiclass
    clus
vv   ALMS1 MUTATED ALMS1 WILD-TYPE
  T1            12             172
  T2             9              85
  T3             2              77
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V5, binary
                 cls
clus                0   1
  ALMS1 MUTATED    14   0
  ALMS1 WILD-TYPE 240   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALMS1 MUTATED     14    0
  ALMS1 WILD-TYPE  240    4
   clus
vv  ALMS1 MUTATED ALMS1 WILD-TYPE
  0            14             240
  1             0               4
[1] 2 2
[1] FALSE
D45V6, binary
                 cls
clus                0   1
  ALMS1 MUTATED    17   0
  ALMS1 WILD-TYPE 252   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALMS1 MUTATED     17    0
  ALMS1 WILD-TYPE  252    4
   clus
vv  ALMS1 MUTATED ALMS1 WILD-TYPE
  0            17             252
  1             0               4
[1] 2 2
[1] FALSE
D45V7, binary
                 cls
clus                0   1
  ALMS1 MUTATED     8  16
  ALMS1 WILD-TYPE 113 236
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALMS1 MUTATED      8   16
  ALMS1 WILD-TYPE  113  236
        clus
vv       ALMS1 MUTATED ALMS1 WILD-TYPE
  FEMALE             8             113
  MALE              16             236
[1] 2 2
[1] FALSE
D45V8, binary
                 cls
clus                0   1
  ALMS1 MUTATED    23   0
  ALMS1 WILD-TYPE 318   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALMS1 MUTATED     23    0
  ALMS1 WILD-TYPE  318    9
     clus
vv    ALMS1 MUTATED ALMS1 WILD-TYPE
  NO             23             318
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  ALMS1 MUTATED                         0                       24
  ALMS1 WILD-TYPE                       3                      339
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  ALMS1 MUTATED                                  0
  ALMS1 WILD-TYPE                                7
D45V9, multiclass
                                  clus
vv                                 ALMS1 MUTATED ALMS1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                    24             339
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ALMS1 MUTATED    23   1   0   0
  ALMS1 WILD-TYPE 304  15   1  22
D45V10, multiclass
    clus
vv   ALMS1 MUTATED ALMS1 WILD-TYPE
  R0            23             304
  R1             1              15
  R2             0               1
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALMS1 MUTATED                                  0    10
  ALMS1 WILD-TYPE                                2   150
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ALMS1 MUTATED                           1    11
  ALMS1 WILD-TYPE                        16   173
D45V11, multiclass
                                  clus
vv                                 ALMS1 MUTATED ALMS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                       10             150
  BLACK OR AFRICAN AMERICAN                    1              16
  WHITE                                       11             173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V12, binary
                 cls
clus                0   1
  ALMS1 MUTATED     1  21
  ALMS1 WILD-TYPE  17 316
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALMS1 MUTATED      1   21
  ALMS1 WILD-TYPE   17  316
                        clus
vv                       ALMS1 MUTATED ALMS1 WILD-TYPE
  HISPANIC OR LATINO                 1              17
  NOT HISPANIC OR LATINO            21             316
[1] 2 2
[1] FALSE

Clustering(46) Variable = NUCB2 MUTATION ANALYSIS
D46V1, survival
                 sevent
clus2               0   1
  NUCB2 MUTATED     0   3
  NUCB2 WILD-TYPE 237 127
  NUCB2 MUTATED NUCB2 WILD-TYPE 
              3             364 
  NUCB2 MUTATED NUCB2 WILD-TYPE 
              3             127 
$`NUCB2 MUTATED`
TCGA-CC-A3MA TCGA-DD-A119 TCGA-DD-A3A0 
        9.96         7.33        25.81 

$`NUCB2 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB 
        4.24         3.35         7.20         3.32         9.86        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
       11.93        11.41         9.99         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        9.83        12.00        13.12        12.56         8.61         9.14 
TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.86         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A 
       79.73        37.78        83.57        53.33       113.00         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.69         5.62        19.76         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ 
       32.52        21.70        30.97        26.37        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       34.49        20.91         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
       14.33        66.67        15.58        18.21        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        89.69        82.62        59.93        72.39 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        60.99        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        20.61        19.59         0.62        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 
       14.40        60.89        23.97        19.10        27.88        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.03         0.33         0.39        13.68        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       28.27        14.86        21.53        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        25.25        22.95        24.46        20.42        17.10 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       14.70        20.78        11.87        14.14        15.78        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80        12.23        13.55         0.89        11.64         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        28.90         1.02         2.20         2.99        37.71 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06        16.83        11.80        27.25        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        26.27        17.69        21.01         3.09 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        15.52        36.10        27.88        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        1.71        15.98        10.75        11.34         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       20.22        24.85        18.28        33.86        30.41        22.78 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       13.55        35.77        25.71        23.21        35.87        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        79.30        11.21 

  NUCB2 MUTATED NUCB2 WILD-TYPE 
           7.33            0.03 
  NUCB2 MUTATED NUCB2 WILD-TYPE 
          25.81          120.82 
  NUCB2 MUTATED NUCB2 WILD-TYPE 
          9.960          19.775 
[1] "7.3 - 25.8 (10.0)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "4.7"
D46V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  NUCB2 MUTATED         1        0         0          1          0          0
  NUCB2 WILD-TYPE     173       86         3         63          9          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  NUCB2 MUTATED          1         0         0
  NUCB2 WILD-TYPE        1         1         2
D46V3, multiclass
            clus
vv           NUCB2 MUTATED NUCB2 WILD-TYPE
  STAGE I                1             173
  STAGE II               0              86
  STAGE III              0               3
  STAGE IIIA             1              63
  STAGE IIIB             0               9
  STAGE IIIC             0               9
  STAGE IV               1               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NUCB2 MUTATED     1   0   2   0
  NUCB2 WILD-TYPE 183  94  77  13
D46V4, multiclass
    clus
vv   NUCB2 MUTATED NUCB2 WILD-TYPE
  T1             1             183
  T2             0              94
  T3             2              77
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V5, binary
                 cls
clus                0   1
  NUCB2 MUTATED     2   0
  NUCB2 WILD-TYPE 252   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUCB2 MUTATED      2    0
  NUCB2 WILD-TYPE  252    4
   clus
vv  NUCB2 MUTATED NUCB2 WILD-TYPE
  0             2             252
  1             0               4
[1] 2 2
[1] FALSE
D46V6, binary
                 cls
clus                0   1
  NUCB2 MUTATED     2   1
  NUCB2 WILD-TYPE 267   3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUCB2 MUTATED      2    1
  NUCB2 WILD-TYPE  267    3
   clus
vv  NUCB2 MUTATED NUCB2 WILD-TYPE
  0             2             267
  1             1               3
[1] 2 2
[1] FALSE
D46V7, binary
                 cls
clus                0   1
  NUCB2 MUTATED     0   3
  NUCB2 WILD-TYPE 121 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUCB2 MUTATED      0    3
  NUCB2 WILD-TYPE  121  249
        clus
vv       NUCB2 MUTATED NUCB2 WILD-TYPE
  FEMALE             0             121
  MALE               3             249
[1] 2 2
[1] FALSE
D46V8, binary
                 cls
clus                0   1
  NUCB2 MUTATED     2   0
  NUCB2 WILD-TYPE 339   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUCB2 MUTATED      2    0
  NUCB2 WILD-TYPE  339    9
     clus
vv    NUCB2 MUTATED NUCB2 WILD-TYPE
  NO              2             339
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  NUCB2 MUTATED                         0                        3
  NUCB2 WILD-TYPE                       3                      360
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  NUCB2 MUTATED                                  0
  NUCB2 WILD-TYPE                                7
D46V9, multiclass
                                  clus
vv                                 NUCB2 MUTATED NUCB2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                     3             360
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NUCB2 MUTATED     2   0   1   0
  NUCB2 WILD-TYPE 325  16   0  22
D46V10, multiclass
    clus
vv   NUCB2 MUTATED NUCB2 WILD-TYPE
  R0             2             325
  R1             0              16
  R2             1               0
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUCB2 MUTATED                                  0     2
  NUCB2 WILD-TYPE                                2   158
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NUCB2 MUTATED                           0     1
  NUCB2 WILD-TYPE                        17   183
D46V11, multiclass
                                  clus
vv                                 NUCB2 MUTATED NUCB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        2             158
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        1             183
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V12, binary
                 cls
clus                0   1
  NUCB2 MUTATED     0   3
  NUCB2 WILD-TYPE  18 334
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUCB2 MUTATED      0    3
  NUCB2 WILD-TYPE   18  334
                        clus
vv                       NUCB2 MUTATED NUCB2 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             3             334
[1] 2 2
[1] FALSE

Clustering(47) Variable = BAZ2A MUTATION ANALYSIS
D47V1, survival
                 sevent
clus2               0   1
  BAZ2A MUTATED     2   9
  BAZ2A WILD-TYPE 235 121
  BAZ2A MUTATED BAZ2A WILD-TYPE 
             11             356 
  BAZ2A MUTATED BAZ2A WILD-TYPE 
              9             121 
$`BAZ2A MUTATED`
TCGA-ES-A2HS TCGA-2Y-A9GS TCGA-DD-A1EE TCGA-DD-A39Y TCGA-DD-AADP TCGA-EP-A2KB 
       22.62        23.80        11.47         5.62        15.06        19.59 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25Y TCGA-G3-A3CJ TCGA-ZP-A9D2 
       14.40        19.10        14.86        19.53        25.15 

$`BAZ2A WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 
       21.17        21.83        18.90        23.64         9.96         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
      120.82        40.41        56.91        49.84        47.74        18.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       20.81        22.92         1.18         8.55        13.02        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 
       10.59         0.66        17.10        14.76         1.51        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.38         1.12        44.42        45.93         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       14.60        18.48        44.81        13.45         0.66         4.24 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
        8.22         2.86         3.19         3.39         4.24         3.35 
TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        7.20         3.32         9.86         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS 
       12.00        13.12        12.56         8.61         9.14         9.86 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       21.70        30.97        26.37        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        40.08        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AADR 
       20.91         0.39        29.52        14.89        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       25.08        26.63        25.78        50.33        35.08        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       89.69        82.62        59.93        72.39        80.71        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        60.99 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        9.73         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 
       20.61         0.62        11.93        60.89        23.97        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
       53.79        28.27        21.53        25.64         5.92        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       25.25        22.95        24.46        20.42        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       20.78        11.87        14.14        15.78        15.65        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       12.23        13.55         0.89        11.64         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       58.88        26.27        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        22.78        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       35.77        25.71        23.21        35.87        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  BAZ2A MUTATED BAZ2A WILD-TYPE 
           5.62            0.03 
  BAZ2A MUTATED BAZ2A WILD-TYPE 
          25.15          120.82 
  BAZ2A MUTATED BAZ2A WILD-TYPE 
          19.10           19.99 
[1] "5.6 - 25.1 (19.1)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "3.4"
D47V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  BAZ2A MUTATED         7        1         0          1          0          0
  BAZ2A WILD-TYPE     167       85         3         63          9          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  BAZ2A MUTATED          0         0         0
  BAZ2A WILD-TYPE        2         1         2
D47V3, multiclass
            clus
vv           BAZ2A MUTATED BAZ2A WILD-TYPE
  STAGE I                7             167
  STAGE II               1              85
  STAGE III              0               3
  STAGE IIIA             1              63
  STAGE IIIB             0               9
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BAZ2A MUTATED     7   3   1   0
  BAZ2A WILD-TYPE 177  91  78  13
D47V4, multiclass
    clus
vv   BAZ2A MUTATED BAZ2A WILD-TYPE
  T1             7             177
  T2             3              91
  T3             1              78
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V5, binary
                 cls
clus                0   1
  BAZ2A MUTATED     5   0
  BAZ2A WILD-TYPE 249   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAZ2A MUTATED      5    0
  BAZ2A WILD-TYPE  249    4
   clus
vv  BAZ2A MUTATED BAZ2A WILD-TYPE
  0             5             249
  1             0               4
[1] 2 2
[1] FALSE
D47V6, binary
                 cls
clus                0   1
  BAZ2A MUTATED     6   0
  BAZ2A WILD-TYPE 263   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAZ2A MUTATED      6    0
  BAZ2A WILD-TYPE  263    4
   clus
vv  BAZ2A MUTATED BAZ2A WILD-TYPE
  0             6             263
  1             0               4
[1] 2 2
[1] FALSE
D47V7, binary
                 cls
clus                0   1
  BAZ2A MUTATED     2   9
  BAZ2A WILD-TYPE 119 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAZ2A MUTATED      2    9
  BAZ2A WILD-TYPE  119  243
        clus
vv       BAZ2A MUTATED BAZ2A WILD-TYPE
  FEMALE             2             119
  MALE               9             243
[1] 2 2
[1] FALSE
D47V8, binary
                 cls
clus                0   1
  BAZ2A MUTATED     9   0
  BAZ2A WILD-TYPE 332   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAZ2A MUTATED      9    0
  BAZ2A WILD-TYPE  332    9
     clus
vv    BAZ2A MUTATED BAZ2A WILD-TYPE
  NO              9             332
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  BAZ2A MUTATED                         0                       11
  BAZ2A WILD-TYPE                       3                      352
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  BAZ2A MUTATED                                  0
  BAZ2A WILD-TYPE                                7
D47V9, multiclass
                                  clus
vv                                 BAZ2A MUTATED BAZ2A WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                    11             352
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BAZ2A MUTATED    10   0   0   1
  BAZ2A WILD-TYPE 317  16   1  21
D47V10, multiclass
    clus
vv   BAZ2A MUTATED BAZ2A WILD-TYPE
  R0            10             317
  R1             0              16
  R2             0               1
  RX             1              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BAZ2A MUTATED                                  1     3
  BAZ2A WILD-TYPE                                1   157
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BAZ2A MUTATED                           1     6
  BAZ2A WILD-TYPE                        16   178
D47V11, multiclass
                                  clus
vv                                 BAZ2A MUTATED BAZ2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               1
  ASIAN                                        3             157
  BLACK OR AFRICAN AMERICAN                    1              16
  WHITE                                        6             178
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V12, binary
                 cls
clus                0   1
  BAZ2A MUTATED     1  10
  BAZ2A WILD-TYPE  17 327
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAZ2A MUTATED      1   10
  BAZ2A WILD-TYPE   17  327
                        clus
vv                       BAZ2A MUTATED BAZ2A WILD-TYPE
  HISPANIC OR LATINO                 1              17
  NOT HISPANIC OR LATINO            10             327
[1] 2 2
[1] FALSE

Clustering(48) Variable = TAF1B MUTATION ANALYSIS
D48V1, survival
                 sevent
clus2               0   1
  TAF1B MUTATED     2   4
  TAF1B WILD-TYPE 235 126
  TAF1B MUTATED TAF1B WILD-TYPE 
              6             361 
  TAF1B MUTATED TAF1B WILD-TYPE 
              4             126 
$`TAF1B MUTATED`
TCGA-DD-A1EG TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-G3-A3CJ TCGA-KR-A7K2 
       45.11         5.62        25.81         7.66        19.53        27.25 

$`TAF1B WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       21.34         9.83        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
        9.14         9.86         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.15        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65        11.47        12.95 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       27.19        55.69        19.76        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       21.70        30.97        26.37        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        40.08        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        29.52        14.89        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       66.67        15.58        18.21        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 
       18.15        20.98        18.61        19.99         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       15.72        25.08        26.63        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       90.48        89.69        82.62        59.93        72.39        80.71 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       60.99        53.69        29.92        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         9.73         0.20        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       13.15        13.41        13.35         1.84         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       19.99        20.61        19.59         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI 
       14.86        21.53        25.64         5.92        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
       22.95        24.46        20.42        17.10        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       11.87        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       11.80        29.79        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       22.95        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       17.69        21.01         3.09         0.72         0.49         0.30 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.04        19.33        19.04        15.39        15.52        36.10 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       27.88        19.76        16.44         1.71        15.98        10.75 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       11.34         0.99        12.99        20.22        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        22.78        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.21        35.87        25.15        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  TAF1B MUTATED TAF1B WILD-TYPE 
           5.62            0.03 
  TAF1B MUTATED TAF1B WILD-TYPE 
          45.11          120.82 
  TAF1B MUTATED TAF1B WILD-TYPE 
          22.67           19.76 
[1] "5.6 - 45.1 (22.7)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "2.2"
D48V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TAF1B MUTATED         4        1         0          1          0          0
  TAF1B WILD-TYPE     170       85         3         63          9          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  TAF1B MUTATED          0         0         0
  TAF1B WILD-TYPE        2         1         2
D48V3, multiclass
            clus
vv           TAF1B MUTATED TAF1B WILD-TYPE
  STAGE I                4             170
  STAGE II               1              85
  STAGE III              0               3
  STAGE IIIA             1              63
  STAGE IIIB             0               9
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TAF1B MUTATED     4   1   1   0
  TAF1B WILD-TYPE 180  93  78  13
D48V4, multiclass
    clus
vv   TAF1B MUTATED TAF1B WILD-TYPE
  T1             4             180
  T2             1              93
  T3             1              78
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V5, binary
                 cls
clus                0   1
  TAF1B MUTATED     4   0
  TAF1B WILD-TYPE 250   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1B MUTATED      4    0
  TAF1B WILD-TYPE  250    4
   clus
vv  TAF1B MUTATED TAF1B WILD-TYPE
  0             4             250
  1             0               4
[1] 2 2
[1] FALSE
D48V6, binary
                 cls
clus                0   1
  TAF1B MUTATED     6   0
  TAF1B WILD-TYPE 263   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1B MUTATED      6    0
  TAF1B WILD-TYPE  263    4
   clus
vv  TAF1B MUTATED TAF1B WILD-TYPE
  0             6             263
  1             0               4
[1] 2 2
[1] FALSE
D48V7, binary
                 cls
clus                0   1
  TAF1B MUTATED     0   6
  TAF1B WILD-TYPE 121 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1B MUTATED      0    6
  TAF1B WILD-TYPE  121  246
        clus
vv       TAF1B MUTATED TAF1B WILD-TYPE
  FEMALE             0             121
  MALE               6             246
[1] 2 2
[1] FALSE
D48V8, binary
                 cls
clus                0   1
  TAF1B MUTATED     6   0
  TAF1B WILD-TYPE 335   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1B MUTATED      6    0
  TAF1B WILD-TYPE  335    9
     clus
vv    TAF1B MUTATED TAF1B WILD-TYPE
  NO              6             335
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  TAF1B MUTATED                         0                        5
  TAF1B WILD-TYPE                       3                      358
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  TAF1B MUTATED                                  1
  TAF1B WILD-TYPE                                6
D48V9, multiclass
                                  clus
vv                                 TAF1B MUTATED TAF1B WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                     5             358
  HEPATOCHOLANGIOCARCINOMA (MIXED)             1               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TAF1B MUTATED     6   0   0   0
  TAF1B WILD-TYPE 321  16   1  22
D48V10, multiclass
    clus
vv   TAF1B MUTATED TAF1B WILD-TYPE
  R0             6             321
  R1             0              16
  R2             0               1
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAF1B MUTATED                                  1     1
  TAF1B WILD-TYPE                                1   159
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TAF1B MUTATED                           0     3
  TAF1B WILD-TYPE                        17   181
D48V11, multiclass
                                  clus
vv                                 TAF1B MUTATED TAF1B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               1
  ASIAN                                        1             159
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        3             181
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V12, binary
                 cls
clus                0   1
  TAF1B MUTATED     0   4
  TAF1B WILD-TYPE  18 333
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1B MUTATED      0    4
  TAF1B WILD-TYPE   18  333
                        clus
vv                       TAF1B MUTATED TAF1B WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             4             333
[1] 2 2
[1] FALSE

Clustering(49) Variable = C1ORF125 MUTATION ANALYSIS
D49V1, survival
                    sevent
clus2                  0   1
  C1ORF125 MUTATED     6   5
  C1ORF125 WILD-TYPE 231 125
  C1ORF125 MUTATED C1ORF125 WILD-TYPE 
                11                356 
  C1ORF125 MUTATED C1ORF125 WILD-TYPE 
                 5                125 
$`C1ORF125 MUTATED`
TCGA-BC-A112 TCGA-G3-A3CG TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-AAD8 TCGA-DD-AADM 
        5.03        22.13        55.69        19.76        40.08         0.39 
TCGA-DD-AADU TCGA-DD-AAE4 TCGA-DD-AAVV TCGA-EP-A2KC TCGA-G3-A5SM 
       18.21        19.99        80.71         0.62        17.10 

$`C1ORF125 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
        6.38        81.73        30.74        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
        2.14        31.27        12.72        24.56         0.76         7.04 
TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
       10.32        44.02        29.52         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
      120.82        40.41        56.91        49.84        47.74        18.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       20.81        22.92         1.18         8.55        13.02        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 
       10.59         0.66        17.10        14.76         1.51        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.38         1.12        44.42        45.93         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       14.60        18.48        44.81        13.45         0.66         4.24 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
        8.22         2.86         3.19         3.39         4.24         3.35 
TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        7.20         3.32         9.86         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS 
       12.00        13.12        12.56         8.61         9.14         9.86 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
        5.62        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       21.70        30.97        26.37        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       22.09        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       29.52        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       19.30        18.25        18.25        18.15        20.98        18.61 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        23.74        15.72        25.08        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        90.48        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       72.39        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        60.99        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        19.99        20.61        19.59        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A7M5 TCGA-G3-A7M6 
       25.25        22.95        24.46        20.42        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       11.87        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  C1ORF125 MUTATED C1ORF125 WILD-TYPE 
              0.39               0.03 
  C1ORF125 MUTATED C1ORF125 WILD-TYPE 
             80.71             120.82 
  C1ORF125 MUTATED C1ORF125 WILD-TYPE 
            19.760             19.775 
[1] "0.4 - 80.7 (19.8)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.5"
D49V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  C1ORF125 MUTATED         5        5         0          0          0
  C1ORF125 WILD-TYPE     169       81         3         64          9
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  C1ORF125 MUTATED            0        0         0         0
  C1ORF125 WILD-TYPE          9        2         1         2
D49V3, multiclass
            clus
vv           C1ORF125 MUTATED C1ORF125 WILD-TYPE
  STAGE I                   5                169
  STAGE II                  5                 81
  STAGE III                 0                  3
  STAGE IIIA                0                 64
  STAGE IIIB                0                  9
  STAGE IIIC                0                  9
  STAGE IV                  0                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C1ORF125 MUTATED     5   5   1   0
  C1ORF125 WILD-TYPE 179  89  78  13
D49V4, multiclass
    clus
vv   C1ORF125 MUTATED C1ORF125 WILD-TYPE
  T1                5                179
  T2                5                 89
  T3                1                 78
  T4                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V5, binary
                    cls
clus                   0   1
  C1ORF125 MUTATED     6   0
  C1ORF125 WILD-TYPE 248   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF125 MUTATED      6    0
  C1ORF125 WILD-TYPE  248    4
   clus
vv  C1ORF125 MUTATED C1ORF125 WILD-TYPE
  0                6                248
  1                0                  4
[1] 2 2
[1] FALSE
D49V6, binary
                    cls
clus                   0   1
  C1ORF125 MUTATED     9   0
  C1ORF125 WILD-TYPE 260   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF125 MUTATED      9    0
  C1ORF125 WILD-TYPE  260    4
   clus
vv  C1ORF125 MUTATED C1ORF125 WILD-TYPE
  0                9                260
  1                0                  4
[1] 2 2
[1] FALSE
D49V7, binary
                    cls
clus                   0   1
  C1ORF125 MUTATED     4   7
  C1ORF125 WILD-TYPE 117 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF125 MUTATED      4    7
  C1ORF125 WILD-TYPE  117  245
        clus
vv       C1ORF125 MUTATED C1ORF125 WILD-TYPE
  FEMALE                4                117
  MALE                  7                245
[1] 2 2
[1] FALSE
D49V8, binary
                    cls
clus                   0   1
  C1ORF125 MUTATED    10   0
  C1ORF125 WILD-TYPE 331   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF125 MUTATED     10    0
  C1ORF125 WILD-TYPE  331    9
     clus
vv    C1ORF125 MUTATED C1ORF125 WILD-TYPE
  NO                10                331
  YES                0                  9
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  C1ORF125 MUTATED                         0                       11
  C1ORF125 WILD-TYPE                       3                      352
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  C1ORF125 MUTATED                                  0
  C1ORF125 WILD-TYPE                                7
D49V9, multiclass
                                  clus
vv                                 C1ORF125 MUTATED C1ORF125 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  3
  HEPATOCELLULAR CARCINOMA                       11                352
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C1ORF125 MUTATED    10   1   0   0
  C1ORF125 WILD-TYPE 317  15   1  22
D49V10, multiclass
    clus
vv   C1ORF125 MUTATED C1ORF125 WILD-TYPE
  R0               10                317
  R1                1                 15
  R2                0                  1
  RX                0                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C1ORF125 MUTATED                                  0     5
  C1ORF125 WILD-TYPE                                2   155
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C1ORF125 MUTATED                           1     4
  C1ORF125 WILD-TYPE                        16   180
D49V11, multiclass
                                  clus
vv                                 C1ORF125 MUTATED C1ORF125 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           5                155
  BLACK OR AFRICAN AMERICAN                       1                 16
  WHITE                                           4                180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V12, binary
                    cls
clus                   0   1
  C1ORF125 MUTATED     0  10
  C1ORF125 WILD-TYPE  18 327
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF125 MUTATED      0   10
  C1ORF125 WILD-TYPE   18  327
                        clus
vv                       C1ORF125 MUTATED C1ORF125 WILD-TYPE
  HISPANIC OR LATINO                    0                 18
  NOT HISPANIC OR LATINO               10                327
[1] 2 2
[1] FALSE

Clustering(50) Variable = AR MUTATION ANALYSIS
D50V1, survival
              sevent
clus2            0   1
  AR MUTATED     4   6
  AR WILD-TYPE 233 124
  AR MUTATED AR WILD-TYPE 
          10          357 
  AR MUTATED AR WILD-TYPE 
           6          124 
$`AR MUTATED`
TCGA-BC-A10Z TCGA-CC-A8HU TCGA-DD-A39X TCGA-DD-A4NR TCGA-DD-AADY TCGA-DD-AAEI 
        1.12        11.31        55.69         0.30        18.25        50.33 
TCGA-DD-AAW1 TCGA-EP-A2KB TCGA-QA-A7B7 TCGA-YA-A8S7 
       65.39        19.59         3.09        13.55 

$`AR WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
        2.99        25.32        23.38        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        14.60        18.48        44.81        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.24         8.22         2.86         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.35         7.20         3.32         9.86         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
       11.93        11.41         9.99         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        9.83        12.00        13.12        12.56         8.61         9.14 
TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        9.86         4.60         9.17         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ 
       32.52        21.70        30.97        26.37        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        40.08        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        29.52        14.89        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 
       66.67        15.58        18.21        19.30        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       25.08        26.63        25.78        35.08        90.48        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       82.62        59.93        72.39        80.71        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       64.77        62.47        66.25        60.99        53.69        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       26.93        28.08        13.91        13.35         9.73         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
       12.82         0.20        14.04        13.15        13.41        13.35 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
        1.84         0.20        18.74        19.99        20.61         0.62 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       19.53        19.23        25.25        22.95        24.46        20.42 
TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       17.10        14.70        20.78        11.87        14.14        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.65        11.80        12.23        13.55         0.89        11.64 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 
       37.71        17.06        16.83        11.80        27.25        29.79 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       13.97        12.03         9.57        16.67        22.95        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        7.53        10.85        58.88        26.27        17.69        21.01 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        15.52        36.10        27.88        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        1.71        15.98        10.75        11.34         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       20.22        24.85        18.28        33.86        30.41        22.78 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        25.71        23.21        35.87        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  AR MUTATED AR WILD-TYPE 
        0.30         0.03 
  AR MUTATED AR WILD-TYPE 
       65.39       120.82 
  AR MUTATED AR WILD-TYPE 
       15.90        19.99 
[1] "0.3 - 65.4 (15.9)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "2.1"
D50V2, continuous
              vv
clus           STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AR MUTATED         6        1         0          3          0          0
  AR WILD-TYPE     168       85         3         61          9          9
              vv
clus           STAGE IV STAGE IVA STAGE IVB
  AR MUTATED          0         0         0
  AR WILD-TYPE        2         1         2
D50V3, multiclass
            clus
vv           AR MUTATED AR WILD-TYPE
  STAGE I             6          168
  STAGE II            1           85
  STAGE III           0            3
  STAGE IIIA          3           61
  STAGE IIIB          0            9
  STAGE IIIC          0            9
  STAGE IV            0            2
  STAGE IVA           0            1
  STAGE IVB           0            2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            T1  T2  T3  T4
  AR MUTATED     6   1   3   0
  AR WILD-TYPE 178  93  76  13
D50V4, multiclass
    clus
vv   AR MUTATED AR WILD-TYPE
  T1          6          178
  T2          1           93
  T3          3           76
  T4          0           13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V5, binary
              cls
clus             0   1
  AR MUTATED     7   0
  AR WILD-TYPE 247   4
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      7    0
  AR WILD-TYPE  247    4
   clus
vv  AR MUTATED AR WILD-TYPE
  0          7          247
  1          0            4
[1] 2 2
[1] FALSE
D50V6, binary
              cls
clus             0   1
  AR MUTATED     6   0
  AR WILD-TYPE 263   4
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      6    0
  AR WILD-TYPE  263    4
   clus
vv  AR MUTATED AR WILD-TYPE
  0          6          263
  1          0            4
[1] 2 2
[1] FALSE
D50V7, binary
              cls
clus             0   1
  AR MUTATED     6   4
  AR WILD-TYPE 115 248
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      6    4
  AR WILD-TYPE  115  248
        clus
vv       AR MUTATED AR WILD-TYPE
  FEMALE          6          115
  MALE            4          248
[1] 2 2
[1] FALSE
D50V8, binary
              cls
clus             0   1
  AR MUTATED    10   0
  AR WILD-TYPE 331   9
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED     10    0
  AR WILD-TYPE  331    9
     clus
vv    AR MUTATED AR WILD-TYPE
  NO          10          331
  YES          0            9
[1] 2 2
[1] FALSE
              vv
clus           FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AR MUTATED                         0                       10
  AR WILD-TYPE                       3                      353
              vv
clus           HEPATOCHOLANGIOCARCINOMA (MIXED)
  AR MUTATED                                  0
  AR WILD-TYPE                                7
D50V9, multiclass
                                  clus
vv                                 AR MUTATED AR WILD-TYPE
  FIBROLAMELLAR CARCINOMA                   0            3
  HEPATOCELLULAR CARCINOMA                 10          353
  HEPATOCHOLANGIOCARCINOMA (MIXED)          0            7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            R0  R1  R2  RX
  AR MUTATED     9   0   0   1
  AR WILD-TYPE 318  16   1  21
D50V10, multiclass
    clus
vv   AR MUTATED AR WILD-TYPE
  R0          9          318
  R1          0           16
  R2          0            1
  RX          1           21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  AR MUTATED                                  0     4                         1
  AR WILD-TYPE                                2   156                        16
              vv
clus           WHITE
  AR MUTATED       5
  AR WILD-TYPE   179
D50V11, multiclass
                                  clus
vv                                 AR MUTATED AR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE          0            2
  ASIAN                                     4          156
  BLACK OR AFRICAN AMERICAN                 1           16
  WHITE                                     5          179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V12, binary
              cls
clus             0   1
  AR MUTATED     1   9
  AR WILD-TYPE  17 328
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      1    9
  AR WILD-TYPE   17  328
                        clus
vv                       AR MUTATED AR WILD-TYPE
  HISPANIC OR LATINO              1           17
  NOT HISPANIC OR LATINO          9          328
[1] 2 2
[1] FALSE

Clustering(51) Variable = SPHK1 MUTATION ANALYSIS
D51V1, survival
                 sevent
clus2               0   1
  SPHK1 MUTATED     2   4
  SPHK1 WILD-TYPE 235 126
  SPHK1 MUTATED SPHK1 WILD-TYPE 
              6             361 
  SPHK1 MUTATED SPHK1 WILD-TYPE 
              4             126 
$`SPHK1 MUTATED`
TCGA-DD-AAE8 TCGA-G3-A7M9 TCGA-DD-A116 TCGA-DD-A1EE TCGA-DD-A3A0 TCGA-G3-A3CJ 
       21.83         1.84        53.33        11.47        25.81        19.53 

$`SPHK1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.17        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF 
        6.38        81.73        30.74        22.13        22.06        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
        2.14        31.27        12.72        24.56         0.76         7.04 
TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
       10.32        44.02        29.52         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
      120.82        40.41        56.91        49.84        47.74        18.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       20.81        22.92         1.18         8.55        13.02        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 
       10.59         0.66        17.10        14.76         1.51        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.38         1.12        44.42        45.93         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       14.60        18.48        44.81        13.45         0.66         4.24 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
        8.22         2.86         3.19         3.39         4.24         3.35 
TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        7.20         3.32         9.86         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS 
       12.00        13.12        12.56         8.61         9.14         9.86 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       37.78        83.57       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        12.95        45.11        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       18.35        13.64        21.14        27.19        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.76         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE 
      107.11        13.78        30.61        33.14        32.52        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        26.37        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       35.67       114.35        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       76.41        55.40        12.53        71.80        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       42.81        61.68        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
        0.39        29.52        14.89        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       25.08        26.63        25.78        50.33        35.08        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       89.69        82.62        59.93        72.39        80.71        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        60.99 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        9.73         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.39        13.68        51.06        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       21.53        25.64         5.92        19.23        25.25        22.95 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       24.46        20.42        17.10        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        0.89        11.64         2.14        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       27.25        29.79        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       22.95        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       17.69        21.01         3.09         0.72         0.49         0.30 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.04        19.33        19.04        15.39        15.52        36.10 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       27.88        19.76        16.44         1.71        15.98        10.75 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       11.34         0.99        12.99        20.22        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        22.78        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.21        35.87        25.15        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  SPHK1 MUTATED SPHK1 WILD-TYPE 
           1.84            0.03 
  SPHK1 MUTATED SPHK1 WILD-TYPE 
          53.33          120.82 
  SPHK1 MUTATED SPHK1 WILD-TYPE 
          20.68           19.76 
[1] "1.8 - 53.3 (20.7)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "2.2"
D51V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  SPHK1 MUTATED         2        1         0          2          1          0
  SPHK1 WILD-TYPE     172       85         3         62          8          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  SPHK1 MUTATED          0         0         0
  SPHK1 WILD-TYPE        2         1         2
D51V3, multiclass
            clus
vv           SPHK1 MUTATED SPHK1 WILD-TYPE
  STAGE I                2             172
  STAGE II               1              85
  STAGE III              0               3
  STAGE IIIA             2              62
  STAGE IIIB             1               8
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SPHK1 MUTATED     2   1   3   0
  SPHK1 WILD-TYPE 182  93  76  13
D51V4, multiclass
    clus
vv   SPHK1 MUTATED SPHK1 WILD-TYPE
  T1             2             182
  T2             1              93
  T3             3              76
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V5, binary
                 cls
clus                0   1
  SPHK1 MUTATED     4   0
  SPHK1 WILD-TYPE 250   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPHK1 MUTATED      4    0
  SPHK1 WILD-TYPE  250    4
   clus
vv  SPHK1 MUTATED SPHK1 WILD-TYPE
  0             4             250
  1             0               4
[1] 2 2
[1] FALSE
D51V6, binary
                 cls
clus                0   1
  SPHK1 MUTATED     5   0
  SPHK1 WILD-TYPE 264   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPHK1 MUTATED      5    0
  SPHK1 WILD-TYPE  264    4
   clus
vv  SPHK1 MUTATED SPHK1 WILD-TYPE
  0             5             264
  1             0               4
[1] 2 2
[1] FALSE
D51V7, binary
                 cls
clus                0   1
  SPHK1 MUTATED     0   6
  SPHK1 WILD-TYPE 121 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPHK1 MUTATED      0    6
  SPHK1 WILD-TYPE  121  246
        clus
vv       SPHK1 MUTATED SPHK1 WILD-TYPE
  FEMALE             0             121
  MALE               6             246
[1] 2 2
[1] FALSE
D51V8, binary
                 cls
clus                0   1
  SPHK1 MUTATED     5   1
  SPHK1 WILD-TYPE 336   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPHK1 MUTATED      5    1
  SPHK1 WILD-TYPE  336    8
     clus
vv    SPHK1 MUTATED SPHK1 WILD-TYPE
  NO              5             336
  YES             1               8
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  SPHK1 MUTATED                         0                        6
  SPHK1 WILD-TYPE                       3                      357
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  SPHK1 MUTATED                                  0
  SPHK1 WILD-TYPE                                7
D51V9, multiclass
                                  clus
vv                                 SPHK1 MUTATED SPHK1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                     6             357
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SPHK1 MUTATED     6   0   0   0
  SPHK1 WILD-TYPE 321  16   1  22
D51V10, multiclass
    clus
vv   SPHK1 MUTATED SPHK1 WILD-TYPE
  R0             6             321
  R1             0              16
  R2             0               1
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPHK1 MUTATED                                  1     2
  SPHK1 WILD-TYPE                                1   158
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SPHK1 MUTATED                           0     3
  SPHK1 WILD-TYPE                        17   181
D51V11, multiclass
                                  clus
vv                                 SPHK1 MUTATED SPHK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               1
  ASIAN                                        2             158
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        3             181
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V12, binary
                 cls
clus                0   1
  SPHK1 MUTATED     0   6
  SPHK1 WILD-TYPE  18 331
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPHK1 MUTATED      0    6
  SPHK1 WILD-TYPE   18  331
                        clus
vv                       SPHK1 MUTATED SPHK1 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             6             331
[1] 2 2
[1] FALSE

Clustering(52) Variable = CREB3L3 MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  CREB3L3 MUTATED     3   2
  CREB3L3 WILD-TYPE 234 128
  CREB3L3 MUTATED CREB3L3 WILD-TYPE 
                5               362 
  CREB3L3 MUTATED CREB3L3 WILD-TYPE 
                2               128 
$`CREB3L3 MUTATED`
TCGA-DD-A3A8 TCGA-DD-AACD TCGA-DD-AACI TCGA-G3-AAV3 TCGA-RC-A7S9 
        0.36        12.53        53.19        13.55        21.04 

$`CREB3L3 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       17.98        36.66        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        20.81        22.92         1.18         8.55        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        17.10        14.76         1.51 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        14.60        18.48        44.81        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.24         8.22         2.86         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.35         7.20         3.32         9.86         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
       11.93        11.41         9.99         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        9.83        12.00        13.12        12.56         8.61         9.14 
TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.86         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65        11.47        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       27.19        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       30.61        33.14        32.52        21.70        30.97        26.37 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        75.65        76.41        55.40 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK 
       71.80        12.00        15.42         6.41        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       34.49        20.91         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
       14.33        66.67        15.58        18.21        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        89.69        82.62        59.93        72.39 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        60.99        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        20.61        19.59         0.62        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 
       14.40        60.89        23.97        19.10        27.88        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.03         0.33         0.39        13.68        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       28.27        14.86        21.53        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        25.25        22.95        24.46        20.42        17.10 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       14.70        20.78        11.87        14.14        15.78        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       11.80        12.23         0.89        11.64         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       58.88        26.27        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.49         0.30        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  CREB3L3 MUTATED CREB3L3 WILD-TYPE 
             0.36              0.03 
  CREB3L3 MUTATED CREB3L3 WILD-TYPE 
            53.19            120.82 
  CREB3L3 MUTATED CREB3L3 WILD-TYPE 
           13.550            19.775 
[1] "0.4 - 53.2 (13.6)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.5"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CREB3L3 MUTATED         2        3         0          0          0          0
  CREB3L3 WILD-TYPE     172       83         3         64          9          9
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  CREB3L3 MUTATED          0         0         0
  CREB3L3 WILD-TYPE        2         1         2
D52V3, multiclass
            clus
vv           CREB3L3 MUTATED CREB3L3 WILD-TYPE
  STAGE I                  2               172
  STAGE II                 3                83
  STAGE III                0                 3
  STAGE IIIA               0                64
  STAGE IIIB               0                 9
  STAGE IIIC               0                 9
  STAGE IV                 0                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CREB3L3 MUTATED     2   3   0   0
  CREB3L3 WILD-TYPE 182  91  79  13
D52V4, multiclass
    clus
vv   CREB3L3 MUTATED CREB3L3 WILD-TYPE
  T1               2               182
  T2               3                91
  T3               0                79
  T4               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V5, binary
                   cls
clus                  0   1
  CREB3L3 MUTATED     5   0
  CREB3L3 WILD-TYPE 249   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CREB3L3 MUTATED      5    0
  CREB3L3 WILD-TYPE  249    4
   clus
vv  CREB3L3 MUTATED CREB3L3 WILD-TYPE
  0               5               249
  1               0                 4
[1] 2 2
[1] FALSE
D52V6, binary
                   cls
clus                  0   1
  CREB3L3 MUTATED     5   0
  CREB3L3 WILD-TYPE 264   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CREB3L3 MUTATED      5    0
  CREB3L3 WILD-TYPE  264    4
   clus
vv  CREB3L3 MUTATED CREB3L3 WILD-TYPE
  0               5               264
  1               0                 4
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  CREB3L3 MUTATED     2   3
  CREB3L3 WILD-TYPE 119 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CREB3L3 MUTATED      2    3
  CREB3L3 WILD-TYPE  119  249
        clus
vv       CREB3L3 MUTATED CREB3L3 WILD-TYPE
  FEMALE               2               119
  MALE                 3               249
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                  0   1
  CREB3L3 MUTATED     5   0
  CREB3L3 WILD-TYPE 336   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CREB3L3 MUTATED      5    0
  CREB3L3 WILD-TYPE  336    9
     clus
vv    CREB3L3 MUTATED CREB3L3 WILD-TYPE
  NO                5               336
  YES               0                 9
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  CREB3L3 MUTATED                         0                        5
  CREB3L3 WILD-TYPE                       3                      358
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  CREB3L3 MUTATED                                  0
  CREB3L3 WILD-TYPE                                7
D52V9, multiclass
                                  clus
vv                                 CREB3L3 MUTATED CREB3L3 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 3
  HEPATOCELLULAR CARCINOMA                       5               358
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CREB3L3 MUTATED     5   0   0   0
  CREB3L3 WILD-TYPE 322  16   1  22
D52V10, multiclass
    clus
vv   CREB3L3 MUTATED CREB3L3 WILD-TYPE
  R0               5               322
  R1               0                16
  R2               0                 1
  RX               0                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CREB3L3 MUTATED                                  0     3
  CREB3L3 WILD-TYPE                                2   157
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CREB3L3 MUTATED                           0     2
  CREB3L3 WILD-TYPE                        17   182
D52V11, multiclass
                                  clus
vv                                 CREB3L3 MUTATED CREB3L3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          3               157
  BLACK OR AFRICAN AMERICAN                      0                17
  WHITE                                          2               182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V12, binary
                   cls
clus                  0   1
  CREB3L3 MUTATED     0   5
  CREB3L3 WILD-TYPE  18 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CREB3L3 MUTATED      0    5
  CREB3L3 WILD-TYPE   18  332
                        clus
vv                       CREB3L3 MUTATED CREB3L3 WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO               5               332
[1] 2 2
[1] FALSE

Clustering(53) Variable = LFNG MUTATION ANALYSIS
D53V1, survival
                sevent
clus2              0   1
  LFNG MUTATED     3   4
  LFNG WILD-TYPE 234 126
  LFNG MUTATED LFNG WILD-TYPE 
             7            360 
  LFNG MUTATED LFNG WILD-TYPE 
             4            126 
$`LFNG MUTATED`
TCGA-ES-A2HS TCGA-BD-A3EP TCGA-CC-A3MA TCGA-CC-A7IK TCGA-DD-A4NB TCGA-DD-AAC8 
       22.62        13.45         9.96         8.61        32.52         0.53 
TCGA-G3-AAUZ 
       15.78 

$`LFNG WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 
       21.17        21.83        18.90        23.64         9.96         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        20.81        22.92         1.18         8.55        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        17.10        14.76         1.51 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BW-A5NO TCGA-CC-5258 
       22.36        14.60        18.48        44.81         0.66         4.24 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
        8.22         2.86         3.19         3.39         4.24         3.35 
TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        7.20         3.32         9.86        10.36        11.93        11.41 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
        9.99         8.94         7.13        21.34         9.83        12.00 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU 
       13.12        12.56         9.14         9.86         4.60        11.31 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        9.17         6.94         8.15        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.33       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       11.47        12.95        45.11        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       18.35        13.64        21.14        27.19        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NE 
      102.74       107.11        13.78        30.61        33.14        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        26.37        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
       35.67       114.35        13.48        11.41        75.65        76.41 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        71.80        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
       53.19        69.11         0.30         3.52        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
       61.68        13.64        14.20        59.31        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       50.33        46.82         5.59        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       40.54        40.83        13.97        40.47        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       37.64        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       29.52        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.21        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
       18.61        19.99         4.64        23.74        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       26.63        25.78        50.33        35.08        90.48        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       82.62        59.93        72.39        80.71        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       64.77        62.47        66.25        65.39        60.99        53.69 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       29.92        26.93        28.08        13.91        13.35         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20        12.82         0.20        14.04        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.35         1.84         0.20        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       19.59         0.62        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
       19.10        27.88        12.03         0.03         0.33         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z 
       13.68        51.06        53.79        28.27        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        25.25        22.95 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       24.46        20.42        17.10        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       14.14        15.65        11.80        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       11.64         2.14        11.87        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 
        2.99        37.71        17.06        16.83        11.80        27.25 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       29.79        13.97        12.03         9.57        16.67        22.95 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         7.53        10.85        58.88        26.27        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 
       21.01         3.09         0.72         0.49         0.30        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       19.33        19.04        15.39        15.52        36.10        27.88 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L 
       19.76        16.44         1.71        15.98        10.75        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD 
        0.99        12.99        20.22        24.85        18.28        33.86 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       30.41        22.78        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.87        25.15        12.99        45.57        79.30        11.21 

  LFNG MUTATED LFNG WILD-TYPE 
          0.53           0.03 
  LFNG MUTATED LFNG WILD-TYPE 
         32.52         120.82 
  LFNG MUTATED LFNG WILD-TYPE 
         13.45          19.89 
[1] "0.5 - 32.5 (13.4)"  "0.0 - 120.8 (19.9)"
[1] "hr=" "2.7"
D53V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  LFNG MUTATED         5        0         0          2          0          0
  LFNG WILD-TYPE     169       86         3         62          9          9
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  LFNG MUTATED          0         0         0
  LFNG WILD-TYPE        2         1         2
D53V3, multiclass
            clus
vv           LFNG MUTATED LFNG WILD-TYPE
  STAGE I               5            169
  STAGE II              0             86
  STAGE III             0              3
  STAGE IIIA            2             62
  STAGE IIIB            0              9
  STAGE IIIC            0              9
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LFNG MUTATED     5   0   2   0
  LFNG WILD-TYPE 179  94  77  13
D53V4, multiclass
    clus
vv   LFNG MUTATED LFNG WILD-TYPE
  T1            5            179
  T2            0             94
  T3            2             77
  T4            0             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V5, binary
                cls
clus               0   1
  LFNG MUTATED     6   0
  LFNG WILD-TYPE 248   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  LFNG MUTATED      6    0
  LFNG WILD-TYPE  248    4
   clus
vv  LFNG MUTATED LFNG WILD-TYPE
  0            6            248
  1            0              4
[1] 2 2
[1] FALSE
D53V6, binary
                cls
clus               0   1
  LFNG MUTATED     6   0
  LFNG WILD-TYPE 263   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  LFNG MUTATED      6    0
  LFNG WILD-TYPE  263    4
   clus
vv  LFNG MUTATED LFNG WILD-TYPE
  0            6            263
  1            0              4
[1] 2 2
[1] FALSE
D53V7, binary
                cls
clus               0   1
  LFNG MUTATED     1   6
  LFNG WILD-TYPE 120 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  LFNG MUTATED      1    6
  LFNG WILD-TYPE  120  246
        clus
vv       LFNG MUTATED LFNG WILD-TYPE
  FEMALE            1            120
  MALE              6            246
[1] 2 2
[1] FALSE
D53V8, binary
                cls
clus               0   1
  LFNG MUTATED     6   0
  LFNG WILD-TYPE 335   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  LFNG MUTATED      6    0
  LFNG WILD-TYPE  335    9
     clus
vv    LFNG MUTATED LFNG WILD-TYPE
  NO             6            335
  YES            0              9
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  LFNG MUTATED                         1                        6
  LFNG WILD-TYPE                       2                      357
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  LFNG MUTATED                                  0
  LFNG WILD-TYPE                                7
D53V9, multiclass
                                  clus
vv                                 LFNG MUTATED LFNG WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     1              2
  HEPATOCELLULAR CARCINOMA                    6            357
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  LFNG MUTATED     7   0   0   0
  LFNG WILD-TYPE 320  16   1  22
D53V10, multiclass
    clus
vv   LFNG MUTATED LFNG WILD-TYPE
  R0            7            320
  R1            0             16
  R2            0              1
  RX            0             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LFNG MUTATED                                  0     3
  LFNG WILD-TYPE                                2   157
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LFNG MUTATED                           1     2
  LFNG WILD-TYPE                        16   182
D53V11, multiclass
                                  clus
vv                                 LFNG MUTATED LFNG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       3            157
  BLACK OR AFRICAN AMERICAN                   1             16
  WHITE                                       2            182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V12, binary
                cls
clus               0   1
  LFNG MUTATED     1   6
  LFNG WILD-TYPE  17 331
[1] "tbl2"
                cls
clus             [,1] [,2]
  LFNG MUTATED      1    6
  LFNG WILD-TYPE   17  331
                        clus
vv                       LFNG MUTATED LFNG WILD-TYPE
  HISPANIC OR LATINO                1             17
  NOT HISPANIC OR LATINO            6            331
[1] 2 2
[1] FALSE

Clustering(54) Variable = FZR1 MUTATION ANALYSIS
D54V1, survival
                sevent
clus2              0   1
  FZR1 MUTATED     4   2
  FZR1 WILD-TYPE 233 128
  FZR1 MUTATED FZR1 WILD-TYPE 
             6            361 
  FZR1 MUTATED FZR1 WILD-TYPE 
             2            128 
$`FZR1 MUTATED`
TCGA-DD-A116 TCGA-DD-AACE TCGA-DD-AAEE TCGA-DD-AAVV TCGA-FV-A2QR TCGA-G3-A7M8 
       53.33        71.80        26.63        80.71        19.10        14.14 

$`FZR1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       21.34         9.83        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
        9.14         9.86         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 
        8.15        79.73        37.78        83.57       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65        11.47        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       27.19        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       30.61        33.14        32.52        21.70        30.97        26.37 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       12.53        12.00        15.42         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
        0.30         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       14.20        59.31        51.35        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.05        34.49        20.91         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI 
        4.64        23.74        15.72        25.08        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        89.69        82.62        59.93        72.39 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       60.99        53.69        29.92        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         9.73         0.20        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       13.15        13.41        13.35         1.84         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       19.99        20.61        19.59         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       60.89        23.97        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.39        13.68        51.06        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
       22.95        24.46        20.42        17.10        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       11.87        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        0.89        11.64         2.14        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       27.25        29.79        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       22.95        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       17.69        21.01         3.09         0.72         0.49         0.30 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.04        19.33        19.04        15.39        15.52        36.10 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       27.88        19.76        16.44         1.71        15.98        10.75 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       11.34         0.99        12.99        20.22        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        22.78        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.21        35.87        25.15        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  FZR1 MUTATED FZR1 WILD-TYPE 
         14.14           0.03 
  FZR1 MUTATED FZR1 WILD-TYPE 
         80.71         120.82 
  FZR1 MUTATED FZR1 WILD-TYPE 
         39.98          19.76 
[1] "14.1 - 80.7 (40.0)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1.6"
D54V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  FZR1 MUTATED         4        1         0          1          0          0
  FZR1 WILD-TYPE     170       85         3         63          9          9
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  FZR1 MUTATED          0         0         0
  FZR1 WILD-TYPE        2         1         2
D54V3, multiclass
            clus
vv           FZR1 MUTATED FZR1 WILD-TYPE
  STAGE I               4            170
  STAGE II              1             85
  STAGE III             0              3
  STAGE IIIA            1             63
  STAGE IIIB            0              9
  STAGE IIIC            0              9
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FZR1 MUTATED     4   1   1   0
  FZR1 WILD-TYPE 180  93  78  13
D54V4, multiclass
    clus
vv   FZR1 MUTATED FZR1 WILD-TYPE
  T1            4            180
  T2            1             93
  T3            1             78
  T4            0             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V5, binary
                cls
clus               0   1
  FZR1 MUTATED     5   0
  FZR1 WILD-TYPE 249   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZR1 MUTATED      5    0
  FZR1 WILD-TYPE  249    4
   clus
vv  FZR1 MUTATED FZR1 WILD-TYPE
  0            5            249
  1            0              4
[1] 2 2
[1] FALSE
D54V6, binary
                cls
clus               0   1
  FZR1 MUTATED     5   0
  FZR1 WILD-TYPE 264   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZR1 MUTATED      5    0
  FZR1 WILD-TYPE  264    4
   clus
vv  FZR1 MUTATED FZR1 WILD-TYPE
  0            5            264
  1            0              4
[1] 2 2
[1] FALSE
D54V7, binary
                cls
clus               0   1
  FZR1 MUTATED     0   6
  FZR1 WILD-TYPE 121 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZR1 MUTATED      0    6
  FZR1 WILD-TYPE  121  246
        clus
vv       FZR1 MUTATED FZR1 WILD-TYPE
  FEMALE            0            121
  MALE              6            246
[1] 2 2
[1] FALSE
D54V8, binary
                cls
clus               0   1
  FZR1 MUTATED     5   1
  FZR1 WILD-TYPE 336   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZR1 MUTATED      5    1
  FZR1 WILD-TYPE  336    8
     clus
vv    FZR1 MUTATED FZR1 WILD-TYPE
  NO             5            336
  YES            1              8
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  FZR1 MUTATED                         0                        6
  FZR1 WILD-TYPE                       3                      357
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  FZR1 MUTATED                                  0
  FZR1 WILD-TYPE                                7
D54V9, multiclass
                                  clus
vv                                 FZR1 MUTATED FZR1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              3
  HEPATOCELLULAR CARCINOMA                    6            357
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  FZR1 MUTATED     4   0   0   2
  FZR1 WILD-TYPE 323  16   1  20
D54V10, multiclass
    clus
vv   FZR1 MUTATED FZR1 WILD-TYPE
  R0            4            323
  R1            0             16
  R2            0              1
  RX            2             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FZR1 MUTATED                                  0     5
  FZR1 WILD-TYPE                                2   155
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FZR1 MUTATED                           0     1
  FZR1 WILD-TYPE                        17   183
D54V11, multiclass
                                  clus
vv                                 FZR1 MUTATED FZR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       5            155
  BLACK OR AFRICAN AMERICAN                   0             17
  WHITE                                       1            183
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V12, binary
                cls
clus               0   1
  FZR1 MUTATED     0   6
  FZR1 WILD-TYPE  18 331
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZR1 MUTATED      0    6
  FZR1 WILD-TYPE   18  331
                        clus
vv                       FZR1 MUTATED FZR1 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            6            331
[1] 2 2
[1] FALSE

Clustering(55) Variable = TRIOBP MUTATION ANALYSIS
D55V1, survival
                  sevent
clus2                0   1
  TRIOBP MUTATED     7   4
  TRIOBP WILD-TYPE 230 126
  TRIOBP MUTATED TRIOBP WILD-TYPE 
              11              356 
  TRIOBP MUTATED TRIOBP WILD-TYPE 
               4              126 
$`TRIOBP MUTATED`
TCGA-DD-AAE7 TCGA-ES-A2HS TCGA-2Y-A9H3 TCGA-CC-5258 TCGA-CC-A3MA TCGA-DD-A1EB 
       21.17        22.62        49.84         4.24         9.96        66.31 
TCGA-DD-A1EE TCGA-DD-A73E TCGA-DD-AACA TCGA-EP-A26S TCGA-WQ-A9G7 
       11.47         1.45        75.65        19.99         0.99 

$`TRIOBP WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A3R2 
       21.83        18.90        23.64         9.96         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
       81.73        30.74        22.13        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
        2.14        31.27        12.72        24.56         0.76         7.04 
TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
       10.32        44.02        29.52         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 
      120.82        40.41        56.91        47.74        18.25        20.81 
TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH 
       22.92         1.18         8.55        13.02        10.78        10.59 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q 
        0.66        17.10        14.76         1.51        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       10.13        27.52        27.52         2.99        25.32        23.38 
TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        1.12        44.42        45.93         0.26        22.36        14.60 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5259 TCGA-CC-5260 
       18.48        44.81        13.45         0.66         8.22         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT 
        3.19         3.39         4.24         3.35         7.20         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE 
        9.86        10.36        11.93        11.41         9.99         8.94 
TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ 
        7.13        21.34         9.83        12.00        13.12        12.56 
TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
        8.61         9.14         9.86         4.60        11.31         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        6.94         8.15        79.73        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
      113.00         7.33         2.60         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG 
       90.71        79.40        19.79        75.65        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       27.19        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       30.61        33.14        32.52        21.70        30.97        26.37 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
        9.30        23.05        22.78        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
        0.53        11.41        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       34.49        20.91         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
       14.33        66.67        15.58        18.21        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        89.69        82.62        59.93        72.39 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        60.99        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        20.61        19.59         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       25.25        22.95        24.46        20.42        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       20.78        11.87        14.14        15.78        15.65        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       12.23        13.55         0.89        11.64         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       58.88        26.27        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       15.98        10.75        11.34        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  TRIOBP MUTATED TRIOBP WILD-TYPE 
            0.99             0.03 
  TRIOBP MUTATED TRIOBP WILD-TYPE 
           75.65           120.82 
  TRIOBP MUTATED TRIOBP WILD-TYPE 
           19.99            19.76 
[1] "1.0 - 75.7 (20.0)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.1"
D55V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TRIOBP MUTATED         6        2         0          2          0          0
  TRIOBP WILD-TYPE     168       84         3         62          9          9
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  TRIOBP MUTATED          0         0         0
  TRIOBP WILD-TYPE        2         1         2
D55V3, multiclass
            clus
vv           TRIOBP MUTATED TRIOBP WILD-TYPE
  STAGE I                 6              168
  STAGE II                2               84
  STAGE III               0                3
  STAGE IIIA              2               62
  STAGE IIIB              0                9
  STAGE IIIC              0                9
  STAGE IV                0                2
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIOBP MUTATED     6   2   3   0
  TRIOBP WILD-TYPE 178  92  76  13
D55V4, multiclass
    clus
vv   TRIOBP MUTATED TRIOBP WILD-TYPE
  T1              6              178
  T2              2               92
  T3              3               76
  T4              0               13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V5, binary
                  cls
clus                 0   1
  TRIOBP MUTATED     8   0
  TRIOBP WILD-TYPE 246   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIOBP MUTATED      8    0
  TRIOBP WILD-TYPE  246    4
   clus
vv  TRIOBP MUTATED TRIOBP WILD-TYPE
  0              8              246
  1              0                4
[1] 2 2
[1] FALSE
D55V6, binary
                  cls
clus                 0   1
  TRIOBP MUTATED     8   0
  TRIOBP WILD-TYPE 261   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIOBP MUTATED      8    0
  TRIOBP WILD-TYPE  261    4
   clus
vv  TRIOBP MUTATED TRIOBP WILD-TYPE
  0              8              261
  1              0                4
[1] 2 2
[1] FALSE
D55V7, binary
                  cls
clus                 0   1
  TRIOBP MUTATED     2   9
  TRIOBP WILD-TYPE 119 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIOBP MUTATED      2    9
  TRIOBP WILD-TYPE  119  243
        clus
vv       TRIOBP MUTATED TRIOBP WILD-TYPE
  FEMALE              2              119
  MALE                9              243
[1] 2 2
[1] FALSE
D55V8, binary
                  cls
clus                 0   1
  TRIOBP MUTATED    10   0
  TRIOBP WILD-TYPE 331   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIOBP MUTATED     10    0
  TRIOBP WILD-TYPE  331    9
     clus
vv    TRIOBP MUTATED TRIOBP WILD-TYPE
  NO              10              331
  YES              0                9
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  TRIOBP MUTATED                         0                       11
  TRIOBP WILD-TYPE                       3                      352
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  TRIOBP MUTATED                                  0
  TRIOBP WILD-TYPE                                7
D55V9, multiclass
                                  clus
vv                                 TRIOBP MUTATED TRIOBP WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                3
  HEPATOCELLULAR CARCINOMA                     11              352
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TRIOBP MUTATED     9   0   0   1
  TRIOBP WILD-TYPE 318  16   1  21
D55V10, multiclass
    clus
vv   TRIOBP MUTATED TRIOBP WILD-TYPE
  R0              9              318
  R1              0               16
  R2              0                1
  RX              1               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIOBP MUTATED                                  0     4
  TRIOBP WILD-TYPE                                2   156
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIOBP MUTATED                           0     6
  TRIOBP WILD-TYPE                        17   178
D55V11, multiclass
                                  clus
vv                                 TRIOBP MUTATED TRIOBP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         4              156
  BLACK OR AFRICAN AMERICAN                     0               17
  WHITE                                         6              178
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V12, binary
                  cls
clus                 0   1
  TRIOBP MUTATED     1   9
  TRIOBP WILD-TYPE  17 328
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIOBP MUTATED      1    9
  TRIOBP WILD-TYPE   17  328
                        clus
vv                       TRIOBP MUTATED TRIOBP WILD-TYPE
  HISPANIC OR LATINO                  1               17
  NOT HISPANIC OR LATINO              9              328
[1] 2 2
[1] FALSE

Clustering(56) Variable = GJB1 MUTATION ANALYSIS
D56V1, survival
                sevent
clus2              0   1
  GJB1 MUTATED     1   2
  GJB1 WILD-TYPE 236 128
  GJB1 MUTATED GJB1 WILD-TYPE 
             3            364 
  GJB1 MUTATED GJB1 WILD-TYPE 
             2            128 
$`GJB1 MUTATED`
TCGA-DD-A1EJ TCGA-DD-AACK TCGA-G3-AAV6 
       33.04         0.30         2.14 

$`GJB1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       21.34         9.83        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
        9.14         9.86         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.15        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65        11.47        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       45.11        49.15         6.02        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       27.19        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       30.61        33.14        32.52        21.70        30.97        26.37 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        71.80        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
       69.11         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       14.20        59.31        51.35        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.05        34.49        20.91         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        23.74        15.72        25.08        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        90.48        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.39        80.71        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        60.99        53.69        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       28.08        13.91        13.35         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20        14.04        13.15        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        20.61        19.59         0.62 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       19.53        19.23        25.25        22.95        24.46        20.42 
TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       17.10        14.70        20.78        11.87        14.14        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.65        11.80        12.23        13.55         0.89        11.64 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        28.90         1.02         2.20         2.99        37.71 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06        16.83        11.80        27.25        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        26.27        17.69        21.01         3.09 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        15.52        36.10        27.88        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        1.71        15.98        10.75        11.34         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       20.22        24.85        18.28        33.86        30.41        22.78 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       13.55        35.77        25.71        23.21        35.87        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        79.30        11.21 

  GJB1 MUTATED GJB1 WILD-TYPE 
          0.30           0.03 
  GJB1 MUTATED GJB1 WILD-TYPE 
         33.04         120.82 
  GJB1 MUTATED GJB1 WILD-TYPE 
         2.140         19.775 
[1] "0.3 - 33.0 (2.1)"   "0.0 - 120.8 (19.8)"
[1] "hr=" "4"  
D56V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  GJB1 MUTATED         1        0         0          1          0          1
  GJB1 WILD-TYPE     173       86         3         63          9          8
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  GJB1 MUTATED          0         0         0
  GJB1 WILD-TYPE        2         1         2
D56V3, multiclass
            clus
vv           GJB1 MUTATED GJB1 WILD-TYPE
  STAGE I               1            173
  STAGE II              0             86
  STAGE III             0              3
  STAGE IIIA            1             63
  STAGE IIIB            0              9
  STAGE IIIC            1              8
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GJB1 MUTATED     2   0   1   0
  GJB1 WILD-TYPE 182  94  78  13
D56V4, multiclass
    clus
vv   GJB1 MUTATED GJB1 WILD-TYPE
  T1            2            182
  T2            0             94
  T3            1             78
  T4            0             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V5, binary
                cls
clus               0   1
  GJB1 MUTATED     2   1
  GJB1 WILD-TYPE 252   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  GJB1 MUTATED      2    1
  GJB1 WILD-TYPE  252    3
   clus
vv  GJB1 MUTATED GJB1 WILD-TYPE
  0            2            252
  1            1              3
[1] 2 2
[1] FALSE
D56V6, binary
                cls
clus               0   1
  GJB1 MUTATED     3   0
  GJB1 WILD-TYPE 266   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  GJB1 MUTATED      3    0
  GJB1 WILD-TYPE  266    4
   clus
vv  GJB1 MUTATED GJB1 WILD-TYPE
  0            3            266
  1            0              4
[1] 2 2
[1] FALSE
D56V7, binary
                cls
clus               0   1
  GJB1 MUTATED     2   1
  GJB1 WILD-TYPE 119 251
[1] "tbl2"
                cls
clus             [,1] [,2]
  GJB1 MUTATED      2    1
  GJB1 WILD-TYPE  119  251
        clus
vv       GJB1 MUTATED GJB1 WILD-TYPE
  FEMALE            2            119
  MALE              1            251
[1] 2 2
[1] FALSE
D56V8, binary
                cls
clus               0   1
  GJB1 MUTATED     3   0
  GJB1 WILD-TYPE 338   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  GJB1 MUTATED      3    0
  GJB1 WILD-TYPE  338    9
     clus
vv    GJB1 MUTATED GJB1 WILD-TYPE
  NO             3            338
  YES            0              9
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  GJB1 MUTATED                         0                        3
  GJB1 WILD-TYPE                       3                      360
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  GJB1 MUTATED                                  0
  GJB1 WILD-TYPE                                7
D56V9, multiclass
                                  clus
vv                                 GJB1 MUTATED GJB1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              3
  HEPATOCELLULAR CARCINOMA                    3            360
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GJB1 MUTATED     3   0   0   0
  GJB1 WILD-TYPE 324  16   1  22
D56V10, multiclass
    clus
vv   GJB1 MUTATED GJB1 WILD-TYPE
  R0            3            324
  R1            0             16
  R2            0              1
  RX            0             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GJB1 MUTATED                                  0     1
  GJB1 WILD-TYPE                                2   159
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GJB1 MUTATED                           0     2
  GJB1 WILD-TYPE                        17   182
D56V11, multiclass
                                  clus
vv                                 GJB1 MUTATED GJB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1            159
  BLACK OR AFRICAN AMERICAN                   0             17
  WHITE                                       2            182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V12, binary
                cls
clus               0   1
  GJB1 MUTATED     0   3
  GJB1 WILD-TYPE  18 334
[1] "tbl2"
                cls
clus             [,1] [,2]
  GJB1 MUTATED      0    3
  GJB1 WILD-TYPE   18  334
                        clus
vv                       GJB1 MUTATED GJB1 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            3            334
[1] 2 2
[1] FALSE

Clustering(57) Variable = DYRK1A MUTATION ANALYSIS
D57V1, survival
                  sevent
clus2                0   1
  DYRK1A MUTATED     3   4
  DYRK1A WILD-TYPE 234 126
  DYRK1A MUTATED DYRK1A WILD-TYPE 
               7              360 
  DYRK1A MUTATED DYRK1A WILD-TYPE 
               4              126 
$`DYRK1A MUTATED`
TCGA-4R-AA8I TCGA-EP-A3JL TCGA-CC-A7IL TCGA-DD-A1EG TCGA-DD-AA3A TCGA-DD-AACK 
        8.61         9.96         9.14        45.11        13.48         0.30 
TCGA-DD-AADO 
       14.89 

$`DYRK1A WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        11.74        38.40        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-ES-A2HS TCGA-FV-A3I1 TCGA-FV-A3R2 
       21.83        18.90        23.64        22.62         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
       81.73        30.74        22.13        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
        2.14        31.27        12.72        24.56         0.76         7.04 
TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
       10.32        44.02        29.52         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
      120.82        40.41        56.91        49.84        47.74        18.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       20.81        22.92         1.18         8.55        13.02        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 
       10.59         0.66        17.10        14.76         1.51        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.38         1.12        44.42        45.93         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       14.60        18.48        44.81        13.45         0.66         4.24 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
        8.22         2.86         3.19         3.39         4.24         3.35 
TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        7.20         3.32         9.86         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HS TCGA-CC-A8HT 
       12.00        13.12        12.56         8.61         9.86         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 
       11.31         9.17         6.94         8.15        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        11.47        12.95        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       18.35        13.64        21.14        27.19        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       21.70        30.97        26.37        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
        1.45        35.67       114.35         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       76.41        55.40        12.53        71.80        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
        6.41        53.19        69.11         3.52        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
       61.68        13.64        14.20        59.31        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       50.33        46.82         5.59        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       40.54        40.83        13.97        40.47        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       37.64        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       29.52        15.06        14.33        66.67        15.58        18.21 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       19.30        18.25        18.25        18.15        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       19.99         4.64        23.74        15.72        25.08        26.63 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       25.78        50.33        35.08        90.48        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       59.93        72.39        80.71        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        60.99        53.69        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       26.93        28.08        13.91        13.35         9.73         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
       12.82         0.20        14.04        13.15        13.41        13.35 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        1.84         0.20        18.74        19.99        20.61        19.59 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        0.62        11.93        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S 
       27.88        12.03         0.03         0.33         0.39        13.68 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       51.06        53.79        28.27        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
        5.92        19.53        19.23        25.25        22.95        24.46 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       20.42        17.10        14.70        20.78        11.87        14.14 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       15.78        15.65        11.80        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       11.64         2.14        11.87        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 
        2.99        37.71        17.06        16.83        11.80        27.25 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       29.79        13.97        12.03         9.57        16.67        22.95 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         7.53        10.85        58.88        26.27        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 
       21.01         3.09         0.72         0.49         0.30        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       19.33        19.04        15.39        15.52        36.10        27.88 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L 
       19.76        16.44         1.71        15.98        10.75        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD 
        0.99        12.99        20.22        24.85        18.28        33.86 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       30.41        22.78        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.87        25.15        12.99        45.57        79.30        11.21 

  DYRK1A MUTATED DYRK1A WILD-TYPE 
            0.30             0.03 
  DYRK1A MUTATED DYRK1A WILD-TYPE 
           45.11           120.82 
  DYRK1A MUTATED DYRK1A WILD-TYPE 
            9.96            19.99 
[1] "0.3 - 45.1 (10.0)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "2.9"
D57V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DYRK1A MUTATED         5        1         0          1          0          0
  DYRK1A WILD-TYPE     169       85         3         63          9          9
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  DYRK1A MUTATED          0         0         0
  DYRK1A WILD-TYPE        2         1         2
D57V3, multiclass
            clus
vv           DYRK1A MUTATED DYRK1A WILD-TYPE
  STAGE I                 5              169
  STAGE II                1               85
  STAGE III               0                3
  STAGE IIIA              1               63
  STAGE IIIB              0                9
  STAGE IIIC              0                9
  STAGE IV                0                2
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DYRK1A MUTATED     5   1   1   0
  DYRK1A WILD-TYPE 179  93  78  13
D57V4, multiclass
    clus
vv   DYRK1A MUTATED DYRK1A WILD-TYPE
  T1              5              179
  T2              1               93
  T3              1               78
  T4              0               13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V5, binary
                  cls
clus                 0   1
  DYRK1A MUTATED     5   0
  DYRK1A WILD-TYPE 249   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DYRK1A MUTATED      5    0
  DYRK1A WILD-TYPE  249    4
   clus
vv  DYRK1A MUTATED DYRK1A WILD-TYPE
  0              5              249
  1              0                4
[1] 2 2
[1] FALSE
D57V6, binary
                  cls
clus                 0   1
  DYRK1A MUTATED     4   0
  DYRK1A WILD-TYPE 265   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DYRK1A MUTATED      4    0
  DYRK1A WILD-TYPE  265    4
   clus
vv  DYRK1A MUTATED DYRK1A WILD-TYPE
  0              4              265
  1              0                4
[1] 2 2
[1] FALSE
D57V7, binary
                  cls
clus                 0   1
  DYRK1A MUTATED     1   6
  DYRK1A WILD-TYPE 120 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DYRK1A MUTATED      1    6
  DYRK1A WILD-TYPE  120  246
        clus
vv       DYRK1A MUTATED DYRK1A WILD-TYPE
  FEMALE              1              120
  MALE                6              246
[1] 2 2
[1] FALSE
D57V8, binary
                  cls
clus                 0   1
  DYRK1A MUTATED     7   0
  DYRK1A WILD-TYPE 334   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DYRK1A MUTATED      7    0
  DYRK1A WILD-TYPE  334    9
     clus
vv    DYRK1A MUTATED DYRK1A WILD-TYPE
  NO               7              334
  YES              0                9
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  DYRK1A MUTATED                         0                        6
  DYRK1A WILD-TYPE                       3                      357
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  DYRK1A MUTATED                                  1
  DYRK1A WILD-TYPE                                6
D57V9, multiclass
                                  clus
vv                                 DYRK1A MUTATED DYRK1A WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                3
  HEPATOCELLULAR CARCINOMA                      6              357
  HEPATOCHOLANGIOCARCINOMA (MIXED)              1                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DYRK1A MUTATED     6   0   0   0
  DYRK1A WILD-TYPE 321  16   1  22
D57V10, multiclass
    clus
vv   DYRK1A MUTATED DYRK1A WILD-TYPE
  R0              6              321
  R1              0               16
  R2              0                1
  RX              0               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DYRK1A MUTATED                                  0     3
  DYRK1A WILD-TYPE                                2   157
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DYRK1A MUTATED                           0     4
  DYRK1A WILD-TYPE                        17   180
D57V11, multiclass
                                  clus
vv                                 DYRK1A MUTATED DYRK1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         3              157
  BLACK OR AFRICAN AMERICAN                     0               17
  WHITE                                         4              180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V12, binary
                  cls
clus                 0   1
  DYRK1A MUTATED     0   7
  DYRK1A WILD-TYPE  18 330
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DYRK1A MUTATED      0    7
  DYRK1A WILD-TYPE   18  330
                        clus
vv                       DYRK1A MUTATED DYRK1A WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              7              330
[1] 2 2
[1] FALSE

Clustering(58) Variable = TNPO1 MUTATION ANALYSIS
D58V1, survival
                 sevent
clus2               0   1
  TNPO1 MUTATED     4   5
  TNPO1 WILD-TYPE 233 125
  TNPO1 MUTATED TNPO1 WILD-TYPE 
              9             358 
  TNPO1 MUTATED TNPO1 WILD-TYPE 
              5             125 
$`TNPO1 MUTATED`
TCGA-FV-A4ZP TCGA-2Y-A9GW TCGA-BC-A10Q TCGA-CC-A7IH TCGA-DD-A116 TCGA-DD-AAW0 
       81.73        41.79        37.32        12.00        53.33        66.25 
TCGA-EP-A12J TCGA-FV-A2QR TCGA-G3-A25U 
       18.74        19.10        53.79 

$`TNPO1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        8.12         6.38        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       23.80        53.39        63.75        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
      120.82        40.41        56.91        49.84        47.74        18.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       20.81        22.92         1.18         8.55        13.02        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 
       10.59         0.66        17.10        14.76         1.51        27.91 
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       10.13        27.52        27.52         2.99        25.32        23.38 
TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        1.12        44.42        45.93         0.26        22.36        14.60 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 
       18.48        44.81        13.45         0.66         4.24         8.22 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 
        2.86         3.19         3.39         4.24         3.35         7.20 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.32         9.86         9.96        10.36        11.93        11.41 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7II 
        9.99         8.94         7.13        21.34         9.83        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU 
       12.56         8.61         9.14         9.86         4.60        11.31 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        9.17         6.94         8.15        79.73        37.78        83.57 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
      113.00         7.33         2.60         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.71        79.40        66.31        19.79        75.65        11.47 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        33.04        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       13.64        21.14        27.19        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE 
      107.11        13.78        30.61        33.14        32.52        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        26.37        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       35.67       114.35        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       76.41        55.40        12.53        71.80        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       42.81        61.68        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
        0.39        29.52        14.89        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       25.08        26.63        25.78        50.33        35.08        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       89.69        82.62        59.93        72.39        80.71        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       56.48        64.77        62.47        65.39        60.99        53.69 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       29.92        26.93        28.08        13.91        13.35         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20        12.82         0.20        14.04        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       13.35         1.84         0.20        19.99        20.61        19.59 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 
        0.62        11.93        14.40        60.89        23.97        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       28.27        14.86        21.53        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        25.25        22.95        24.46        20.42        17.10 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       14.70        20.78        11.87        14.14        15.78        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80        12.23        13.55         0.89        11.64         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        28.90         1.02         2.20         2.99        37.71 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06        16.83        11.80        27.25        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        26.27        17.69        21.01         3.09 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        15.52        36.10        27.88        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        1.71        15.98        10.75        11.34         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       20.22        24.85        18.28        33.86        30.41        22.78 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       13.55        35.77        25.71        23.21        35.87        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        79.30        11.21 

  TNPO1 MUTATED TNPO1 WILD-TYPE 
          12.00            0.03 
  TNPO1 MUTATED TNPO1 WILD-TYPE 
          81.73          120.82 
  TNPO1 MUTATED TNPO1 WILD-TYPE 
         41.790          19.675 
[1] "12.0 - 81.7 (41.8)" "0.0 - 120.8 (19.7)"
[1] "hr=" "1.1"
D58V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TNPO1 MUTATED         5        0         0          3          0          0
  TNPO1 WILD-TYPE     169       86         3         61          9          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  TNPO1 MUTATED          0         0         0
  TNPO1 WILD-TYPE        2         1         2
D58V3, multiclass
            clus
vv           TNPO1 MUTATED TNPO1 WILD-TYPE
  STAGE I                5             169
  STAGE II               0              86
  STAGE III              0               3
  STAGE IIIA             3              61
  STAGE IIIB             0               9
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TNPO1 MUTATED     5   1   3   0
  TNPO1 WILD-TYPE 179  93  76  13
D58V4, multiclass
    clus
vv   TNPO1 MUTATED TNPO1 WILD-TYPE
  T1             5             179
  T2             1              93
  T3             3              76
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V5, binary
                 cls
clus                0   1
  TNPO1 MUTATED     6   0
  TNPO1 WILD-TYPE 248   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNPO1 MUTATED      6    0
  TNPO1 WILD-TYPE  248    4
   clus
vv  TNPO1 MUTATED TNPO1 WILD-TYPE
  0             6             248
  1             0               4
[1] 2 2
[1] FALSE
D58V6, binary
                 cls
clus                0   1
  TNPO1 MUTATED     6   0
  TNPO1 WILD-TYPE 263   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNPO1 MUTATED      6    0
  TNPO1 WILD-TYPE  263    4
   clus
vv  TNPO1 MUTATED TNPO1 WILD-TYPE
  0             6             263
  1             0               4
[1] 2 2
[1] FALSE
D58V7, binary
                 cls
clus                0   1
  TNPO1 MUTATED     2   7
  TNPO1 WILD-TYPE 119 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNPO1 MUTATED      2    7
  TNPO1 WILD-TYPE  119  245
        clus
vv       TNPO1 MUTATED TNPO1 WILD-TYPE
  FEMALE             2             119
  MALE               7             245
[1] 2 2
[1] FALSE
D58V8, binary
                 cls
clus                0   1
  TNPO1 MUTATED     8   1
  TNPO1 WILD-TYPE 333   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNPO1 MUTATED      8    1
  TNPO1 WILD-TYPE  333    8
     clus
vv    TNPO1 MUTATED TNPO1 WILD-TYPE
  NO              8             333
  YES             1               8
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  TNPO1 MUTATED                         0                        9
  TNPO1 WILD-TYPE                       3                      354
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  TNPO1 MUTATED                                  0
  TNPO1 WILD-TYPE                                7
D58V9, multiclass
                                  clus
vv                                 TNPO1 MUTATED TNPO1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                     9             354
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TNPO1 MUTATED     6   2   0   1
  TNPO1 WILD-TYPE 321  14   1  21
D58V10, multiclass
    clus
vv   TNPO1 MUTATED TNPO1 WILD-TYPE
  R0             6             321
  R1             2              14
  R2             0               1
  RX             1              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TNPO1 MUTATED                                  0     4
  TNPO1 WILD-TYPE                                2   156
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TNPO1 MUTATED                           1     4
  TNPO1 WILD-TYPE                        16   180
D58V11, multiclass
                                  clus
vv                                 TNPO1 MUTATED TNPO1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        4             156
  BLACK OR AFRICAN AMERICAN                    1              16
  WHITE                                        4             180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V12, binary
                 cls
clus                0   1
  TNPO1 MUTATED     0   9
  TNPO1 WILD-TYPE  18 328
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNPO1 MUTATED      0    9
  TNPO1 WILD-TYPE   18  328
                        clus
vv                       TNPO1 MUTATED TNPO1 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             9             328
[1] 2 2
[1] FALSE

Clustering(59) Variable = PDZD4 MUTATION ANALYSIS
D59V1, survival
                 sevent
clus2               0   1
  PDZD4 MUTATED     3   1
  PDZD4 WILD-TYPE 234 129
  PDZD4 MUTATED PDZD4 WILD-TYPE 
              4             363 
  PDZD4 MUTATED PDZD4 WILD-TYPE 
              1             129 
$`PDZD4 MUTATED`
TCGA-3K-AAZ8 TCGA-DD-A1EG TCGA-G3-A3CJ TCGA-UB-A7MB 
       13.02        45.11        19.53        19.76 

$`PDZD4 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        17.10        14.76         1.51 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        14.60        18.48        44.81        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.24         8.22         2.86         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.35         7.20         3.32         9.86         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
       11.93        11.41         9.99         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        9.83        12.00        13.12        12.56         8.61         9.14 
TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.86         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH 
       66.31        19.79        75.65        11.47        12.95        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       33.14        32.52        21.70        30.97        26.37        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       23.05        22.78         1.45        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        75.65        76.41        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       71.80        12.00        15.42         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
        0.30         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       14.20        59.31        51.35        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.05        34.49        20.91         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        23.74        15.72        25.08        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        90.48        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.39        80.71        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        60.99        53.69        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       28.08        13.91        13.35         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20        14.04        13.15        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        20.61        19.59         0.62 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        14.86        21.53        25.64         5.92 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        25.25        22.95        24.46        20.42        17.10 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       14.70        20.78        11.87        14.14        15.78        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80        12.23        13.55         0.89        11.64         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        28.90         1.02         2.20         2.99        37.71 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06        16.83        11.80        27.25        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        26.27        17.69        21.01         3.09 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD 
       15.39        15.52        36.10        27.88        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        22.78        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        25.71        23.21        35.87        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  PDZD4 MUTATED PDZD4 WILD-TYPE 
          13.02            0.03 
  PDZD4 MUTATED PDZD4 WILD-TYPE 
          45.11          120.82 
  PDZD4 MUTATED PDZD4 WILD-TYPE 
         19.645          19.790 
[1] "13.0 - 45.1 (19.6)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1.3"
D59V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PDZD4 MUTATED         1        2         0          0          1          0
  PDZD4 WILD-TYPE     173       84         3         64          8          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  PDZD4 MUTATED          0         0         0
  PDZD4 WILD-TYPE        2         1         2
D59V3, multiclass
            clus
vv           PDZD4 MUTATED PDZD4 WILD-TYPE
  STAGE I                1             173
  STAGE II               2              84
  STAGE III              0               3
  STAGE IIIA             0              64
  STAGE IIIB             1               8
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PDZD4 MUTATED     1   2   1   0
  PDZD4 WILD-TYPE 183  92  78  13
D59V4, multiclass
    clus
vv   PDZD4 MUTATED PDZD4 WILD-TYPE
  T1             1             183
  T2             2              92
  T3             1              78
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V5, binary
                 cls
clus                0   1
  PDZD4 MUTATED     2   0
  PDZD4 WILD-TYPE 252   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDZD4 MUTATED      2    0
  PDZD4 WILD-TYPE  252    4
   clus
vv  PDZD4 MUTATED PDZD4 WILD-TYPE
  0             2             252
  1             0               4
[1] 2 2
[1] FALSE
D59V6, binary
                 cls
clus                0   1
  PDZD4 MUTATED     2   0
  PDZD4 WILD-TYPE 267   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDZD4 MUTATED      2    0
  PDZD4 WILD-TYPE  267    4
   clus
vv  PDZD4 MUTATED PDZD4 WILD-TYPE
  0             2             267
  1             0               4
[1] 2 2
[1] FALSE
D59V7, binary
                 cls
clus                0   1
  PDZD4 MUTATED     0   4
  PDZD4 WILD-TYPE 121 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDZD4 MUTATED      0    4
  PDZD4 WILD-TYPE  121  248
        clus
vv       PDZD4 MUTATED PDZD4 WILD-TYPE
  FEMALE             0             121
  MALE               4             248
[1] 2 2
[1] FALSE
D59V8, binary
                 cls
clus                0   1
  PDZD4 MUTATED     4   0
  PDZD4 WILD-TYPE 337   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDZD4 MUTATED      4    0
  PDZD4 WILD-TYPE  337    9
     clus
vv    PDZD4 MUTATED PDZD4 WILD-TYPE
  NO              4             337
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  PDZD4 MUTATED                         0                        4
  PDZD4 WILD-TYPE                       3                      359
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  PDZD4 MUTATED                                  0
  PDZD4 WILD-TYPE                                7
D59V9, multiclass
                                  clus
vv                                 PDZD4 MUTATED PDZD4 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                     4             359
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PDZD4 MUTATED     3   0   0   1
  PDZD4 WILD-TYPE 324  16   1  21
D59V10, multiclass
    clus
vv   PDZD4 MUTATED PDZD4 WILD-TYPE
  R0             3             324
  R1             0              16
  R2             0               1
  RX             1              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PDZD4 MUTATED                                  1     0
  PDZD4 WILD-TYPE                                1   160
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PDZD4 MUTATED                           1     2
  PDZD4 WILD-TYPE                        16   182
D59V11, multiclass
                                  clus
vv                                 PDZD4 MUTATED PDZD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               1
  ASIAN                                        0             160
  BLACK OR AFRICAN AMERICAN                    1              16
  WHITE                                        2             182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V12, binary
                 cls
clus                0   1
  PDZD4 MUTATED     0   4
  PDZD4 WILD-TYPE  18 333
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDZD4 MUTATED      0    4
  PDZD4 WILD-TYPE   18  333
                        clus
vv                       PDZD4 MUTATED PDZD4 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             4             333
[1] 2 2
[1] FALSE

Clustering(60) Variable = CCNA2 MUTATION ANALYSIS
D60V1, survival
                 sevent
clus2               0   1
  CCNA2 MUTATED     1   4
  CCNA2 WILD-TYPE 236 126
  CCNA2 MUTATED CCNA2 WILD-TYPE 
              5             362 
  CCNA2 MUTATED CCNA2 WILD-TYPE 
              4             126 
$`CCNA2 MUTATED`
TCGA-DD-A119 TCGA-DD-A1EG TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-XR-A8TD 
        7.33        45.11         5.62        25.81        33.86 

$`CCNA2 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       21.34         9.83        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
        9.14         9.86         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.15        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH 
       66.31        19.79        75.65        11.47        12.95        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       55.69        19.76         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       21.70        30.97        26.37        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        40.08        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        29.52        14.89        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       66.67        15.58        18.21        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 
       18.15        20.98        18.61        19.99         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       15.72        25.08        26.63        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       90.48        89.69        82.62        59.93        72.39        80.71 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       60.99        53.69        29.92        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         9.73         0.20        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       13.15        13.41        13.35         1.84         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       19.99        20.61        19.59         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       25.25        22.95        24.46        20.42        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       20.78        11.87        14.14        15.78        15.65        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       12.23        13.55         0.89        11.64         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       58.88        26.27        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       24.85        18.28        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  CCNA2 MUTATED CCNA2 WILD-TYPE 
           5.62            0.03 
  CCNA2 MUTATED CCNA2 WILD-TYPE 
          45.11          120.82 
  CCNA2 MUTATED CCNA2 WILD-TYPE 
          25.81           19.76 
[1] "5.6 - 45.1 (25.8)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "2.5"
D60V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CCNA2 MUTATED         3        0         0          0          1          0
  CCNA2 WILD-TYPE     171       86         3         64          8          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  CCNA2 MUTATED          1         0         0
  CCNA2 WILD-TYPE        1         1         2
D60V3, multiclass
            clus
vv           CCNA2 MUTATED CCNA2 WILD-TYPE
  STAGE I                3             171
  STAGE II               0              86
  STAGE III              0               3
  STAGE IIIA             0              64
  STAGE IIIB             1               8
  STAGE IIIC             0               9
  STAGE IV               1               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CCNA2 MUTATED     3   0   2   0
  CCNA2 WILD-TYPE 181  94  77  13
D60V4, multiclass
    clus
vv   CCNA2 MUTATED CCNA2 WILD-TYPE
  T1             3             181
  T2             0              94
  T3             2              77
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V5, binary
                 cls
clus                0   1
  CCNA2 MUTATED     3   0
  CCNA2 WILD-TYPE 251   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCNA2 MUTATED      3    0
  CCNA2 WILD-TYPE  251    4
   clus
vv  CCNA2 MUTATED CCNA2 WILD-TYPE
  0             3             251
  1             0               4
[1] 2 2
[1] FALSE
D60V6, binary
                 cls
clus                0   1
  CCNA2 MUTATED     4   1
  CCNA2 WILD-TYPE 265   3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCNA2 MUTATED      4    1
  CCNA2 WILD-TYPE  265    3
   clus
vv  CCNA2 MUTATED CCNA2 WILD-TYPE
  0             4             265
  1             1               3
[1] 2 2
[1] FALSE
D60V7, binary
                 cls
clus                0   1
  CCNA2 MUTATED     1   4
  CCNA2 WILD-TYPE 120 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCNA2 MUTATED      1    4
  CCNA2 WILD-TYPE  120  248
        clus
vv       CCNA2 MUTATED CCNA2 WILD-TYPE
  FEMALE             1             120
  MALE               4             248
[1] 2 2
[1] FALSE
D60V8, binary
                 cls
clus                0   1
  CCNA2 MUTATED     4   0
  CCNA2 WILD-TYPE 337   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCNA2 MUTATED      4    0
  CCNA2 WILD-TYPE  337    9
     clus
vv    CCNA2 MUTATED CCNA2 WILD-TYPE
  NO              4             337
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  CCNA2 MUTATED                         0                        5
  CCNA2 WILD-TYPE                       3                      358
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  CCNA2 MUTATED                                  0
  CCNA2 WILD-TYPE                                7
D60V9, multiclass
                                  clus
vv                                 CCNA2 MUTATED CCNA2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                     5             358
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CCNA2 MUTATED     4   0   1   0
  CCNA2 WILD-TYPE 323  16   0  22
D60V10, multiclass
    clus
vv   CCNA2 MUTATED CCNA2 WILD-TYPE
  R0             4             323
  R1             0              16
  R2             1               0
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCNA2 MUTATED                                  0     2
  CCNA2 WILD-TYPE                                2   158
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CCNA2 MUTATED                           0     3
  CCNA2 WILD-TYPE                        17   181
D60V11, multiclass
                                  clus
vv                                 CCNA2 MUTATED CCNA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        2             158
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        3             181
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V12, binary
                 cls
clus                0   1
  CCNA2 MUTATED     1   4
  CCNA2 WILD-TYPE  17 333
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCNA2 MUTATED      1    4
  CCNA2 WILD-TYPE   17  333
                        clus
vv                       CCNA2 MUTATED CCNA2 WILD-TYPE
  HISPANIC OR LATINO                 1              17
  NOT HISPANIC OR LATINO             4             333
[1] 2 2
[1] FALSE

Clustering(61) Variable = AHCTF1 MUTATION ANALYSIS
D61V1, survival
                  sevent
clus2                0   1
  AHCTF1 MUTATED     6   2
  AHCTF1 WILD-TYPE 231 128
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
               8              359 
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
               2              128 
$`AHCTF1 MUTATED`
TCGA-2Y-A9H5 TCGA-DD-A113 TCGA-DD-A73E TCGA-DD-AACZ TCGA-DD-AAVX TCGA-G3-AAV0 
       18.25        79.73         1.45         5.62        56.48        15.65 
TCGA-RC-A7SK TCGA-WQ-A9G7 
       15.52         0.99 

$`AHCTF1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       47.74        20.81        22.92         1.18         8.55        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        17.10        14.76         1.51 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        14.60        18.48        44.81        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.24         8.22         2.86         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.35         7.20         3.32         9.86         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
       11.93        11.41         9.99         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        9.83        12.00        13.12        12.56         8.61         9.14 
TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.86         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       33.14        32.52        21.70        30.97        26.37        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       23.05        22.78        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
       47.67         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        40.08        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        29.52        14.89        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       66.67        15.58        18.21        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 
       18.15        20.98        18.61        19.99         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       15.72        25.08        26.63        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       90.48        89.69        82.62        59.93        72.39        80.71 
TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       76.18        64.77        62.47        66.25        65.39        60.99 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        9.73         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.39        13.68        51.06        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
       22.95        24.46        20.42        17.10        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       11.87        14.14        15.78        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        0.89        11.64         2.14        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       27.25        29.79        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       22.95        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       17.69        21.01         3.09         0.72         0.49         0.30 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MA 
       21.04        19.33        19.04        15.39        36.10        27.88 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L 
       19.76        16.44         1.71        15.98        10.75        11.34 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE 
       12.99        20.22        24.85        18.28        33.86        30.41 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       22.78        13.55        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        79.30        11.21 

  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
            0.99             0.03 
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
           79.73           120.82 
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
          15.585           19.990 
[1] "1.0 - 79.7 (15.6)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "1.2"
D61V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AHCTF1 MUTATED         5        2         0          0          0          0
  AHCTF1 WILD-TYPE     169       84         3         64          9          9
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  AHCTF1 MUTATED          0         0         0
  AHCTF1 WILD-TYPE        2         1         2
D61V3, multiclass
            clus
vv           AHCTF1 MUTATED AHCTF1 WILD-TYPE
  STAGE I                 5              169
  STAGE II                2               84
  STAGE III               0                3
  STAGE IIIA              0               64
  STAGE IIIB              0                9
  STAGE IIIC              0                9
  STAGE IV                0                2
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  AHCTF1 MUTATED     5   2   1   0
  AHCTF1 WILD-TYPE 179  92  78  13
D61V4, multiclass
    clus
vv   AHCTF1 MUTATED AHCTF1 WILD-TYPE
  T1              5              179
  T2              2               92
  T3              1               78
  T4              0               13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V5, binary
                  cls
clus                 0   1
  AHCTF1 MUTATED     7   0
  AHCTF1 WILD-TYPE 247   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHCTF1 MUTATED      7    0
  AHCTF1 WILD-TYPE  247    4
   clus
vv  AHCTF1 MUTATED AHCTF1 WILD-TYPE
  0              7              247
  1              0                4
[1] 2 2
[1] FALSE
D61V6, binary
                  cls
clus                 0   1
  AHCTF1 MUTATED     7   0
  AHCTF1 WILD-TYPE 262   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHCTF1 MUTATED      7    0
  AHCTF1 WILD-TYPE  262    4
   clus
vv  AHCTF1 MUTATED AHCTF1 WILD-TYPE
  0              7              262
  1              0                4
[1] 2 2
[1] FALSE
D61V7, binary
                  cls
clus                 0   1
  AHCTF1 MUTATED     4   4
  AHCTF1 WILD-TYPE 117 248
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHCTF1 MUTATED      4    4
  AHCTF1 WILD-TYPE  117  248
        clus
vv       AHCTF1 MUTATED AHCTF1 WILD-TYPE
  FEMALE              4              117
  MALE                4              248
[1] 2 2
[1] FALSE
D61V8, binary
                  cls
clus                 0   1
  AHCTF1 MUTATED     7   1
  AHCTF1 WILD-TYPE 334   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHCTF1 MUTATED      7    1
  AHCTF1 WILD-TYPE  334    8
     clus
vv    AHCTF1 MUTATED AHCTF1 WILD-TYPE
  NO               7              334
  YES              1                8
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AHCTF1 MUTATED                         0                        8
  AHCTF1 WILD-TYPE                       3                      355
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  AHCTF1 MUTATED                                  0
  AHCTF1 WILD-TYPE                                7
D61V9, multiclass
                                  clus
vv                                 AHCTF1 MUTATED AHCTF1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                3
  HEPATOCELLULAR CARCINOMA                      8              355
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  AHCTF1 MUTATED     8   0   0   0
  AHCTF1 WILD-TYPE 319  16   1  22
D61V10, multiclass
    clus
vv   AHCTF1 MUTATED AHCTF1 WILD-TYPE
  R0              8              319
  R1              0               16
  R2              0                1
  RX              0               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AHCTF1 MUTATED                                  0     4
  AHCTF1 WILD-TYPE                                2   156
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  AHCTF1 MUTATED                           0     4
  AHCTF1 WILD-TYPE                        17   180
D61V11, multiclass
                                  clus
vv                                 AHCTF1 MUTATED AHCTF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         4              156
  BLACK OR AFRICAN AMERICAN                     0               17
  WHITE                                         4              180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V12, binary
                  cls
clus                 0   1
  AHCTF1 MUTATED     0   8
  AHCTF1 WILD-TYPE  18 329
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHCTF1 MUTATED      0    8
  AHCTF1 WILD-TYPE   18  329
                        clus
vv                       AHCTF1 MUTATED AHCTF1 WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              8              329
[1] 2 2
[1] FALSE

Clustering(62) Variable = RXRB MUTATION ANALYSIS
D62V1, survival
                sevent
clus2              0   1
  RXRB MUTATED     2   6
  RXRB WILD-TYPE 235 124
  RXRB MUTATED RXRB WILD-TYPE 
             8            359 
  RXRB MUTATED RXRB WILD-TYPE 
             6            124 
$`RXRB MUTATED`
TCGA-2Y-A9GZ TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EJ TCGA-DD-A3A0 TCGA-DD-AAEE 
       27.88        11.47        45.11        33.04        25.81        26.63 
TCGA-WQ-A9G7 TCGA-WX-AA47 
        0.99        18.28 

$`RXRB WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       24.89       120.82        40.41        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        20.81        22.92         1.18         8.55        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        17.10        14.76         1.51 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        14.60        18.48        44.81        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.24         8.22         2.86         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.35         7.20         3.32         9.86         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
       11.93        11.41         9.99         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        9.83        12.00        13.12        12.56         8.61         9.14 
TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.86         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.79        75.65        12.95        49.15         6.02 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       18.35        13.64        21.14        27.19        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.76         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE 
      107.11        13.78        30.61        33.14        32.52        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        26.37        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       35.67       114.35        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       76.41        55.40        12.53        71.80        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       42.81        61.68        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
        0.39        29.52        14.89        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       25.08        25.78        50.33        35.08        90.48        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       82.62        59.93        72.39        80.71        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       64.77        62.47        66.25        65.39        60.99        53.69 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       29.92        26.93        28.08        13.91        13.35         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20        12.82         0.20        14.04        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.35         1.84         0.20        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       19.59         0.62        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
       19.10        27.88        12.03         0.03         0.33         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z 
       13.68        51.06        53.79        28.27        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        25.25        22.95 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       24.46        20.42        17.10        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        0.89        11.64         2.14        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       27.25        29.79        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       22.95        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       17.69        21.01         3.09         0.72         0.49         0.30 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.04        19.33        19.04        15.39        15.52        36.10 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       27.88        19.76        16.44         1.71        15.98        10.75 
TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-XR-A8TD TCGA-XR-A8TE 
       11.34        12.99        20.22        24.85        33.86        30.41 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       22.78        13.55        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        79.30        11.21 

  RXRB MUTATED RXRB WILD-TYPE 
          0.99           0.03 
  RXRB MUTATED RXRB WILD-TYPE 
         45.11         120.82 
  RXRB MUTATED RXRB WILD-TYPE 
         26.22          19.76 
[1] "1.0 - 45.1 (26.2)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "2.3"
D62V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  RXRB MUTATED         3        1         0          2          0          1
  RXRB WILD-TYPE     171       85         3         62          9          8
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  RXRB MUTATED          0         0         0
  RXRB WILD-TYPE        2         1         2
D62V3, multiclass
            clus
vv           RXRB MUTATED RXRB WILD-TYPE
  STAGE I               3            171
  STAGE II              1             85
  STAGE III             0              3
  STAGE IIIA            2             62
  STAGE IIIB            0              9
  STAGE IIIC            1              8
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RXRB MUTATED     4   1   3   0
  RXRB WILD-TYPE 180  93  76  13
D62V4, multiclass
    clus
vv   RXRB MUTATED RXRB WILD-TYPE
  T1            4            180
  T2            1             93
  T3            3             76
  T4            0             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V5, binary
                cls
clus               0   1
  RXRB MUTATED     3   1
  RXRB WILD-TYPE 251   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  RXRB MUTATED      3    1
  RXRB WILD-TYPE  251    3
   clus
vv  RXRB MUTATED RXRB WILD-TYPE
  0            3            251
  1            1              3
[1] 2 2
[1] FALSE
D62V6, binary
                cls
clus               0   1
  RXRB MUTATED     6   0
  RXRB WILD-TYPE 263   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  RXRB MUTATED      6    0
  RXRB WILD-TYPE  263    4
   clus
vv  RXRB MUTATED RXRB WILD-TYPE
  0            6            263
  1            0              4
[1] 2 2
[1] FALSE
D62V7, binary
                cls
clus               0   1
  RXRB MUTATED     4   4
  RXRB WILD-TYPE 117 248
[1] "tbl2"
                cls
clus             [,1] [,2]
  RXRB MUTATED      4    4
  RXRB WILD-TYPE  117  248
        clus
vv       RXRB MUTATED RXRB WILD-TYPE
  FEMALE            4            117
  MALE              4            248
[1] 2 2
[1] FALSE
D62V8, binary
                cls
clus               0   1
  RXRB MUTATED     7   1
  RXRB WILD-TYPE 334   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  RXRB MUTATED      7    1
  RXRB WILD-TYPE  334    8
     clus
vv    RXRB MUTATED RXRB WILD-TYPE
  NO             7            334
  YES            1              8
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  RXRB MUTATED                         0                        8
  RXRB WILD-TYPE                       3                      355
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  RXRB MUTATED                                  0
  RXRB WILD-TYPE                                7
D62V9, multiclass
                                  clus
vv                                 RXRB MUTATED RXRB WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              3
  HEPATOCELLULAR CARCINOMA                    8            355
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RXRB MUTATED     8   0   0   0
  RXRB WILD-TYPE 319  16   1  22
D62V10, multiclass
    clus
vv   RXRB MUTATED RXRB WILD-TYPE
  R0            8            319
  R1            0             16
  R2            0              1
  RX            0             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RXRB MUTATED                                  0     1
  RXRB WILD-TYPE                                2   159
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RXRB MUTATED                           0     7
  RXRB WILD-TYPE                        17   177
D62V11, multiclass
                                  clus
vv                                 RXRB MUTATED RXRB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1            159
  BLACK OR AFRICAN AMERICAN                   0             17
  WHITE                                       7            177
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V12, binary
                cls
clus               0   1
  RXRB MUTATED     0   8
  RXRB WILD-TYPE  18 329
[1] "tbl2"
                cls
clus             [,1] [,2]
  RXRB MUTATED      0    8
  RXRB WILD-TYPE   18  329
                        clus
vv                       RXRB MUTATED RXRB WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            8            329
[1] 2 2
[1] FALSE

Clustering(63) Variable = PARP1 MUTATION ANALYSIS
D63V1, survival
                 sevent
clus2               0   1
  PARP1 MUTATED     3   2
  PARP1 WILD-TYPE 234 128
  PARP1 MUTATED PARP1 WILD-TYPE 
              5             362 
  PARP1 MUTATED PARP1 WILD-TYPE 
              2             128 
$`PARP1 MUTATED`
TCGA-4R-AA8I TCGA-BC-A3KG TCGA-DD-A1EG TCGA-G3-A3CJ TCGA-WQ-A9G7 
        8.61        22.36        45.11        19.53         0.99 

$`PARP1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        11.74        38.40        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        20.81        22.92         1.18         8.55        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        17.10        14.76         1.51 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       14.60        18.48        44.81        13.45         0.66         4.24 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
        8.22         2.86         3.19         3.39         4.24         3.35 
TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        7.20         3.32         9.86         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS 
       12.00        13.12        12.56         8.61         9.14         9.86 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        11.47        12.95        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ 
       32.52        21.70        30.97        26.37        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       34.49        20.91         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
       14.33        66.67        15.58        18.21        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        89.69        82.62        59.93        72.39 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        60.99        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        20.61        19.59         0.62        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 
       14.40        60.89        23.97        19.10        27.88        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.03         0.33         0.39        13.68        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
       28.27        14.86        21.53        25.64         5.92        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       25.25        22.95        24.46        20.42        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       20.78        11.87        14.14        15.78        15.65        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       12.23        13.55         0.89        11.64         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       58.88        26.27        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       15.98        10.75        11.34        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  PARP1 MUTATED PARP1 WILD-TYPE 
           0.99            0.03 
  PARP1 MUTATED PARP1 WILD-TYPE 
          45.11          120.82 
  PARP1 MUTATED PARP1 WILD-TYPE 
         19.530          19.775 
[1] "1.0 - 45.1 (19.5)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.6"
D63V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PARP1 MUTATED         1        3         0          0          0          0
  PARP1 WILD-TYPE     173       83         3         64          9          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  PARP1 MUTATED          0         0         0
  PARP1 WILD-TYPE        2         1         2
D63V3, multiclass
            clus
vv           PARP1 MUTATED PARP1 WILD-TYPE
  STAGE I                1             173
  STAGE II               3              83
  STAGE III              0               3
  STAGE IIIA             0              64
  STAGE IIIB             0               9
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PARP1 MUTATED     1   3   1   0
  PARP1 WILD-TYPE 183  91  78  13
D63V4, multiclass
    clus
vv   PARP1 MUTATED PARP1 WILD-TYPE
  T1             1             183
  T2             3              91
  T3             1              78
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V5, binary
                 cls
clus                0   1
  PARP1 MUTATED     3   0
  PARP1 WILD-TYPE 251   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARP1 MUTATED      3    0
  PARP1 WILD-TYPE  251    4
   clus
vv  PARP1 MUTATED PARP1 WILD-TYPE
  0             3             251
  1             0               4
[1] 2 2
[1] FALSE
D63V6, binary
                 cls
clus                0   1
  PARP1 MUTATED     4   0
  PARP1 WILD-TYPE 265   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARP1 MUTATED      4    0
  PARP1 WILD-TYPE  265    4
   clus
vv  PARP1 MUTATED PARP1 WILD-TYPE
  0             4             265
  1             0               4
[1] 2 2
[1] FALSE
D63V7, binary
                 cls
clus                0   1
  PARP1 MUTATED     2   3
  PARP1 WILD-TYPE 119 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARP1 MUTATED      2    3
  PARP1 WILD-TYPE  119  249
        clus
vv       PARP1 MUTATED PARP1 WILD-TYPE
  FEMALE             2             119
  MALE               3             249
[1] 2 2
[1] FALSE
D63V8, binary
                 cls
clus                0   1
  PARP1 MUTATED     5   0
  PARP1 WILD-TYPE 336   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARP1 MUTATED      5    0
  PARP1 WILD-TYPE  336    9
     clus
vv    PARP1 MUTATED PARP1 WILD-TYPE
  NO              5             336
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  PARP1 MUTATED                         0                        5
  PARP1 WILD-TYPE                       3                      358
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  PARP1 MUTATED                                  0
  PARP1 WILD-TYPE                                7
D63V9, multiclass
                                  clus
vv                                 PARP1 MUTATED PARP1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                     5             358
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PARP1 MUTATED     5   0   0   0
  PARP1 WILD-TYPE 322  16   1  22
D63V10, multiclass
    clus
vv   PARP1 MUTATED PARP1 WILD-TYPE
  R0             5             322
  R1             0              16
  R2             0               1
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PARP1 MUTATED                                  1     0
  PARP1 WILD-TYPE                                1   160
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PARP1 MUTATED                           0     4
  PARP1 WILD-TYPE                        17   180
D63V11, multiclass
                                  clus
vv                                 PARP1 MUTATED PARP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               1
  ASIAN                                        0             160
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        4             180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V12, binary
                 cls
clus                0   1
  PARP1 MUTATED     0   5
  PARP1 WILD-TYPE  18 332
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARP1 MUTATED      0    5
  PARP1 WILD-TYPE   18  332
                        clus
vv                       PARP1 MUTATED PARP1 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             5             332
[1] 2 2
[1] FALSE

Clustering(64) Variable = NBEA MUTATION ANALYSIS
D64V1, survival
                sevent
clus2              0   1
  NBEA MUTATED    10  10
  NBEA WILD-TYPE 227 120
  NBEA MUTATED NBEA WILD-TYPE 
            20            347 
  NBEA MUTATED NBEA WILD-TYPE 
            10            120 
$`NBEA MUTATED`
TCGA-4R-AA8I TCGA-ES-A2HS TCGA-UB-A7MF TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-BC-A3KG 
        8.61        22.62         7.04        56.91        47.74        22.36 
TCGA-CC-5261 TCGA-CC-A3MB TCGA-CC-A5UD TCGA-DD-A1EE TCGA-DD-AACP TCGA-DD-AAD2 
        3.19        10.36         9.99        11.47        13.64        21.63 
TCGA-DD-AADB TCGA-DD-AAE4 TCGA-DD-AAVP TCGA-EP-A2KA TCGA-EP-A2KB TCGA-G3-A25S 
       40.83        19.99        90.48        20.61        19.59        13.68 
TCGA-G3-A25U TCGA-G3-A25Z 
       53.79        21.53 

$`NBEA WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        11.74        38.40        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A3R2 
       21.83        18.90        23.64         9.96         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
       81.73        30.74        22.13        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-AA0V 
        2.14        31.27        12.72        24.56         0.76        10.32 
TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT 
       44.02        29.52         0.69        40.80        23.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 
       63.75        41.79        80.28        24.89        27.88       120.82 
TCGA-2Y-A9H1 TCGA-2Y-A9H3 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       40.41        49.84        18.25        20.81        22.92         1.18 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C 
        8.55        13.02        10.78        10.59         0.66        17.10 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T 
       14.76         1.51        27.91        37.32        10.13        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 
       27.52         2.99        25.32        23.38         1.12        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
       45.93         0.26        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-5263 
        0.66         4.24         8.22         2.86         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC 
        3.35         7.20         3.32         9.86         9.96        11.93 
TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
       11.41         8.94         7.13        21.34         9.83        12.00 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT 
       13.12        12.56         8.61         9.14         9.86         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 
       11.31         9.17         6.94         8.15        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        12.95        45.11        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       18.35        13.64        21.14        27.19        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       21.70        30.97        26.37        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       58.16        42.81        61.68        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
        4.50        18.54        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.54        13.97        40.47        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       35.67        35.05        34.49        20.91         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       14.89        15.06        14.33        66.67        15.58        18.21 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       19.30        18.25        18.25        18.15        20.98        18.61 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        23.74        15.72        25.08        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       50.33        35.08        89.69        82.62        59.93        72.39 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        60.99        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       18.74        19.99         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A3CI 
        0.39        51.06        28.27        14.86        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       19.53        19.23        25.25        22.95        24.46        20.42 
TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       17.10        14.70        20.78        11.87        14.14        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.65        11.80        12.23        13.55         0.89        11.64 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 
       37.71        17.06        16.83        11.80        27.25        29.79 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       13.97        12.03         9.57        16.67        22.95        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        7.53        10.85        58.88        26.27        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB 
        3.09         0.72         0.49         0.30        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.04        15.39        15.52        36.10        27.88        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 
       16.44         1.71        15.98        10.75        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE 
       12.99        20.22        24.85        18.28        33.86        30.41 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       22.78        13.55        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        79.30        11.21 

  NBEA MUTATED NBEA WILD-TYPE 
          3.19           0.03 
  NBEA MUTATED NBEA WILD-TYPE 
         90.48         120.82 
  NBEA MUTATED NBEA WILD-TYPE 
         20.30          19.76 
[1] "3.2 - 90.5 (20.3)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.5"
D64V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  NBEA MUTATED        13        3         0          5          0          0
  NBEA WILD-TYPE     161       83         3         59          9          9
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  NBEA MUTATED          0         0         0
  NBEA WILD-TYPE        2         1         2
D64V3, multiclass
            clus
vv           NBEA MUTATED NBEA WILD-TYPE
  STAGE I              13            161
  STAGE II              3             83
  STAGE III             0              3
  STAGE IIIA            5             59
  STAGE IIIB            0              9
  STAGE IIIC            0              9
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NBEA MUTATED    13   3   5   0
  NBEA WILD-TYPE 171  91  74  13
D64V4, multiclass
    clus
vv   NBEA MUTATED NBEA WILD-TYPE
  T1           13            171
  T2            3             91
  T3            5             74
  T4            0             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V5, binary
                cls
clus               0   1
  NBEA MUTATED    15   0
  NBEA WILD-TYPE 239   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  NBEA MUTATED     15    0
  NBEA WILD-TYPE  239    4
   clus
vv  NBEA MUTATED NBEA WILD-TYPE
  0           15            239
  1            0              4
[1] 2 2
[1] FALSE
D64V6, binary
                cls
clus               0   1
  NBEA MUTATED    13   0
  NBEA WILD-TYPE 256   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  NBEA MUTATED     13    0
  NBEA WILD-TYPE  256    4
   clus
vv  NBEA MUTATED NBEA WILD-TYPE
  0           13            256
  1            0              4
[1] 2 2
[1] FALSE
D64V7, binary
                cls
clus               0   1
  NBEA MUTATED     6  15
  NBEA WILD-TYPE 115 237
[1] "tbl2"
                cls
clus             [,1] [,2]
  NBEA MUTATED      6   15
  NBEA WILD-TYPE  115  237
        clus
vv       NBEA MUTATED NBEA WILD-TYPE
  FEMALE            6            115
  MALE             15            237
[1] 2 2
[1] FALSE
D64V8, binary
                cls
clus               0   1
  NBEA MUTATED    19   0
  NBEA WILD-TYPE 322   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  NBEA MUTATED     19    0
  NBEA WILD-TYPE  322    9
     clus
vv    NBEA MUTATED NBEA WILD-TYPE
  NO            19            322
  YES            0              9
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  NBEA MUTATED                         0                       21
  NBEA WILD-TYPE                       3                      342
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  NBEA MUTATED                                  0
  NBEA WILD-TYPE                                7
D64V9, multiclass
                                  clus
vv                                 NBEA MUTATED NBEA WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              3
  HEPATOCELLULAR CARCINOMA                   21            342
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NBEA MUTATED    18   1   0   2
  NBEA WILD-TYPE 309  15   1  20
D64V10, multiclass
    clus
vv   NBEA MUTATED NBEA WILD-TYPE
  R0           18            309
  R1            1             15
  R2            0              1
  RX            2             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NBEA MUTATED                                  0    10
  NBEA WILD-TYPE                                2   150
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NBEA MUTATED                           1    10
  NBEA WILD-TYPE                        16   174
D64V11, multiclass
                                  clus
vv                                 NBEA MUTATED NBEA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                      10            150
  BLACK OR AFRICAN AMERICAN                   1             16
  WHITE                                      10            174
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V12, binary
                cls
clus               0   1
  NBEA MUTATED     0  21
  NBEA WILD-TYPE  18 316
[1] "tbl2"
                cls
clus             [,1] [,2]
  NBEA MUTATED      0   21
  NBEA WILD-TYPE   18  316
                        clus
vv                       NBEA MUTATED NBEA WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO           21            316
[1] 2 2
[1] FALSE

Clustering(65) Variable = H6PD MUTATION ANALYSIS
D65V1, survival
                sevent
clus2              0   1
  H6PD MUTATED     2   3
  H6PD WILD-TYPE 235 127
  H6PD MUTATED H6PD WILD-TYPE 
             5            362 
  H6PD MUTATED H6PD WILD-TYPE 
             3            127 
$`H6PD MUTATED`
TCGA-2Y-A9H8 TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-AACI TCGA-EP-A2KA 
       20.81        79.40        11.47        53.19        20.61 

$`H6PD WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       47.74        18.25        22.92         1.18         8.55        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        17.10        14.76         1.51 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        14.60        18.48        44.81        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.24         8.22         2.86         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.35         7.20         3.32         9.86         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
       11.93        11.41         9.99         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        9.83        12.00        13.12        12.56         8.61         9.14 
TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.86         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EB 
        2.60         0.46        21.76        51.29        90.71        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ 
       32.52        21.70        30.97        26.37        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       12.00        15.42         6.41        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        40.08        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        29.52        14.89        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       66.67        15.58        18.21        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 
       18.15        20.98        18.61        19.99         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       15.72        25.08        26.63        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       90.48        89.69        82.62        59.93        72.39        80.71 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       60.99        53.69        29.92        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         9.73         0.20        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       13.15        13.41        13.35         1.84         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       19.99        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.39        13.68        51.06        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
       22.95        24.46        20.42        17.10        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       11.87        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  H6PD MUTATED H6PD WILD-TYPE 
         11.47           0.03 
  H6PD MUTATED H6PD WILD-TYPE 
         79.40         120.82 
  H6PD MUTATED H6PD WILD-TYPE 
        20.810         19.675 
[1] "11.5 - 79.4 (20.8)" "0.0 - 120.8 (19.7)"
[1] "hr=" "1.4"
D65V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  H6PD MUTATED         0        2         0          2          0          0
  H6PD WILD-TYPE     174       84         3         62          9          9
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  H6PD MUTATED          0         0         0
  H6PD WILD-TYPE        2         1         2
D65V3, multiclass
            clus
vv           H6PD MUTATED H6PD WILD-TYPE
  STAGE I               0            174
  STAGE II              2             84
  STAGE III             0              3
  STAGE IIIA            2             62
  STAGE IIIB            0              9
  STAGE IIIC            0              9
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  H6PD MUTATED     1   2   2   0
  H6PD WILD-TYPE 183  92  77  13
D65V4, multiclass
    clus
vv   H6PD MUTATED H6PD WILD-TYPE
  T1            1            183
  T2            2             92
  T3            2             77
  T4            0             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V5, binary
                cls
clus               0   1
  H6PD MUTATED     3   0
  H6PD WILD-TYPE 251   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  H6PD MUTATED      3    0
  H6PD WILD-TYPE  251    4
   clus
vv  H6PD MUTATED H6PD WILD-TYPE
  0            3            251
  1            0              4
[1] 2 2
[1] FALSE
D65V6, binary
                cls
clus               0   1
  H6PD MUTATED     3   0
  H6PD WILD-TYPE 266   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  H6PD MUTATED      3    0
  H6PD WILD-TYPE  266    4
   clus
vv  H6PD MUTATED H6PD WILD-TYPE
  0            3            266
  1            0              4
[1] 2 2
[1] FALSE
D65V7, binary
                cls
clus               0   1
  H6PD MUTATED     2   3
  H6PD WILD-TYPE 119 249
[1] "tbl2"
                cls
clus             [,1] [,2]
  H6PD MUTATED      2    3
  H6PD WILD-TYPE  119  249
        clus
vv       H6PD MUTATED H6PD WILD-TYPE
  FEMALE            2            119
  MALE              3            249
[1] 2 2
[1] FALSE
D65V8, binary
                cls
clus               0   1
  H6PD MUTATED     5   0
  H6PD WILD-TYPE 336   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  H6PD MUTATED      5    0
  H6PD WILD-TYPE  336    9
     clus
vv    H6PD MUTATED H6PD WILD-TYPE
  NO             5            336
  YES            0              9
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  H6PD MUTATED                         0                        5
  H6PD WILD-TYPE                       3                      358
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  H6PD MUTATED                                  0
  H6PD WILD-TYPE                                7
D65V9, multiclass
                                  clus
vv                                 H6PD MUTATED H6PD WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              3
  HEPATOCELLULAR CARCINOMA                    5            358
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  H6PD MUTATED     5   0   0   0
  H6PD WILD-TYPE 322  16   1  22
D65V10, multiclass
    clus
vv   H6PD MUTATED H6PD WILD-TYPE
  R0            5            322
  R1            0             16
  R2            0              1
  RX            0             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  H6PD MUTATED                                  0     2
  H6PD WILD-TYPE                                2   158
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  H6PD MUTATED                           0     3
  H6PD WILD-TYPE                        17   181
D65V11, multiclass
                                  clus
vv                                 H6PD MUTATED H6PD WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       2            158
  BLACK OR AFRICAN AMERICAN                   0             17
  WHITE                                       3            181
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V12, binary
                cls
clus               0   1
  H6PD MUTATED     0   5
  H6PD WILD-TYPE  18 332
[1] "tbl2"
                cls
clus             [,1] [,2]
  H6PD MUTATED      0    5
  H6PD WILD-TYPE   18  332
                        clus
vv                       H6PD MUTATED H6PD WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            5            332
[1] 2 2
[1] FALSE

Clustering(66) Variable = VPS4B MUTATION ANALYSIS
D66V1, survival
                 sevent
clus2               0   1
  VPS4B MUTATED     2   3
  VPS4B WILD-TYPE 235 127
  VPS4B MUTATED VPS4B WILD-TYPE 
              5             362 
  VPS4B MUTATED VPS4B WILD-TYPE 
              3             127 
$`VPS4B MUTATED`
TCGA-4R-AA8I TCGA-XR-A8TG TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A3A0 
        8.61        29.52        79.40        11.47        25.81 

$`VPS4B WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        11.74        38.40        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
        7.04        10.32        44.02         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
      120.82        40.41        56.91        49.84        47.74        18.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       20.81        22.92         1.18         8.55        13.02        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 
       10.59         0.66        17.10        14.76         1.51        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.38         1.12        44.42        45.93         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       14.60        18.48        44.81        13.45         0.66         4.24 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
        8.22         2.86         3.19         3.39         4.24         3.35 
TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        7.20         3.32         9.86         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS 
       12.00        13.12        12.56         8.61         9.14         9.86 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        21.76        51.29        90.71        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        12.95        45.11        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       18.35        13.64        21.14        27.19        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.76         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE 
      107.11        13.78        30.61        33.14        32.52        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        26.37        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       35.67       114.35        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       76.41        55.40        12.53        71.80        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       42.81        61.68        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
        0.39        29.52        14.89        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       25.08        26.63        25.78        50.33        35.08        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       89.69        82.62        59.93        72.39        80.71        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        60.99 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        9.73         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.39        13.68        51.06        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
       22.95        24.46        20.42        17.10        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       11.87        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  VPS4B MUTATED VPS4B WILD-TYPE 
           8.61            0.03 
  VPS4B MUTATED VPS4B WILD-TYPE 
          79.40          120.82 
  VPS4B MUTATED VPS4B WILD-TYPE 
          25.81           19.76 
[1] "8.6 - 79.4 (25.8)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.6"
D66V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  VPS4B MUTATED         2        2         0          1          0          0
  VPS4B WILD-TYPE     172       84         3         63          9          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  VPS4B MUTATED          0         0         0
  VPS4B WILD-TYPE        2         1         2
D66V3, multiclass
            clus
vv           VPS4B MUTATED VPS4B WILD-TYPE
  STAGE I                2             172
  STAGE II               2              84
  STAGE III              0               3
  STAGE IIIA             1              63
  STAGE IIIB             0               9
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  VPS4B MUTATED     2   2   1   0
  VPS4B WILD-TYPE 182  92  78  13
D66V4, multiclass
    clus
vv   VPS4B MUTATED VPS4B WILD-TYPE
  T1             2             182
  T2             2              92
  T3             1              78
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V5, binary
                 cls
clus                0   1
  VPS4B MUTATED     2   0
  VPS4B WILD-TYPE 252   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS4B MUTATED      2    0
  VPS4B WILD-TYPE  252    4
   clus
vv  VPS4B MUTATED VPS4B WILD-TYPE
  0             2             252
  1             0               4
[1] 2 2
[1] FALSE
D66V6, binary
                 cls
clus                0   1
  VPS4B MUTATED     4   0
  VPS4B WILD-TYPE 265   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS4B MUTATED      4    0
  VPS4B WILD-TYPE  265    4
   clus
vv  VPS4B MUTATED VPS4B WILD-TYPE
  0             4             265
  1             0               4
[1] 2 2
[1] FALSE
D66V7, binary
                 cls
clus                0   1
  VPS4B MUTATED     0   5
  VPS4B WILD-TYPE 121 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS4B MUTATED      0    5
  VPS4B WILD-TYPE  121  247
        clus
vv       VPS4B MUTATED VPS4B WILD-TYPE
  FEMALE             0             121
  MALE               5             247
[1] 2 2
[1] FALSE
D66V8, binary
                 cls
clus                0   1
  VPS4B MUTATED     4   1
  VPS4B WILD-TYPE 337   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS4B MUTATED      4    1
  VPS4B WILD-TYPE  337    8
     clus
vv    VPS4B MUTATED VPS4B WILD-TYPE
  NO              4             337
  YES             1               8
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  VPS4B MUTATED                         0                        5
  VPS4B WILD-TYPE                       3                      358
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  VPS4B MUTATED                                  0
  VPS4B WILD-TYPE                                7
D66V9, multiclass
                                  clus
vv                                 VPS4B MUTATED VPS4B WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                     5             358
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  VPS4B MUTATED     5   0   0   0
  VPS4B WILD-TYPE 322  16   1  22
D66V10, multiclass
    clus
vv   VPS4B MUTATED VPS4B WILD-TYPE
  R0             5             322
  R1             0              16
  R2             0               1
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VPS4B MUTATED                                  0     1
  VPS4B WILD-TYPE                                2   159
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  VPS4B MUTATED                           0     4
  VPS4B WILD-TYPE                        17   180
D66V11, multiclass
                                  clus
vv                                 VPS4B MUTATED VPS4B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1             159
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        4             180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V12, binary
                 cls
clus                0   1
  VPS4B MUTATED     1   4
  VPS4B WILD-TYPE  17 333
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS4B MUTATED      1    4
  VPS4B WILD-TYPE   17  333
                        clus
vv                       VPS4B MUTATED VPS4B WILD-TYPE
  HISPANIC OR LATINO                 1              17
  NOT HISPANIC OR LATINO             4             333
[1] 2 2
[1] FALSE

Clustering(67) Variable = HNRNPL MUTATION ANALYSIS
D67V1, survival
                  sevent
clus2                0   1
  HNRNPL MUTATED     3   5
  HNRNPL WILD-TYPE 234 125
  HNRNPL MUTATED HNRNPL WILD-TYPE 
               8              359 
  HNRNPL MUTATED HNRNPL WILD-TYPE 
               5              125 
$`HNRNPL MUTATED`
TCGA-4R-AA8I TCGA-BC-A216 TCGA-CC-A8HT TCGA-DD-A3A0 TCGA-DD-AACH TCGA-DD-AAD1 
        8.61        44.42         4.60        25.81         6.41        18.54 
TCGA-EP-A12J TCGA-EP-A2KA 
       18.74        20.61 

$`HNRNPL WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        11.74        38.40        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        20.81        22.92         1.18         8.55        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        17.10        14.76         1.51 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       25.32        23.38         1.12        45.93         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       14.60        18.48        44.81        13.45         0.66         4.24 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
        8.22         2.86         3.19         3.39         4.24         3.35 
TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        7.20         3.32         9.86         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS 
       12.00        13.12        12.56         8.61         9.14         9.86 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 
       11.31         9.17         6.94         8.15        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65        11.47        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
        5.62        19.76         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       21.70        30.97        26.37        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
       15.42        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       42.81        61.68        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
        4.50        21.63        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       40.54        40.83        13.97        40.47        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       37.64        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       29.52        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.21        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
       18.61        19.99         4.64        23.74        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       26.63        25.78        50.33        35.08        90.48        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       82.62        59.93        72.39        80.71        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       64.77        62.47        66.25        65.39        60.99        53.69 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       29.92        26.93        28.08        13.91        13.35         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20        12.82         0.20        14.04        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC 
       13.35         1.84         0.20        19.99        19.59         0.62 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       19.53        19.23        25.25        22.95        24.46        20.42 
TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       17.10        14.70        20.78        11.87        14.14        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.65        11.80        12.23        13.55         0.89        11.64 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 
       37.71        17.06        16.83        11.80        27.25        29.79 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I 
       13.97        12.03         9.57        16.67        22.95        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        7.53        10.85        58.88        26.27        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB 
        3.09         0.72         0.49         0.30        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB 
       19.04        15.39        15.52        36.10        27.88        19.76 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 
       16.44         1.71        15.98        10.75        11.34         0.99 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE 
       12.99        20.22        24.85        18.28        33.86        30.41 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       22.78        13.55        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        79.30        11.21 

  HNRNPL MUTATED HNRNPL WILD-TYPE 
            4.60             0.03 
  HNRNPL MUTATED HNRNPL WILD-TYPE 
           44.42           120.82 
  HNRNPL MUTATED HNRNPL WILD-TYPE 
           18.64            19.79 
[1] "4.6 - 44.4 (18.6)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "2.5"
D67V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  HNRNPL MUTATED         3        2         0          3          0          0
  HNRNPL WILD-TYPE     171       84         3         61          9          9
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  HNRNPL MUTATED          0         0         0
  HNRNPL WILD-TYPE        2         1         2
D67V3, multiclass
            clus
vv           HNRNPL MUTATED HNRNPL WILD-TYPE
  STAGE I                 3              171
  STAGE II                2               84
  STAGE III               0                3
  STAGE IIIA              3               61
  STAGE IIIB              0                9
  STAGE IIIC              0                9
  STAGE IV                0                2
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HNRNPL MUTATED     3   2   3   0
  HNRNPL WILD-TYPE 181  92  76  13
D67V4, multiclass
    clus
vv   HNRNPL MUTATED HNRNPL WILD-TYPE
  T1              3              181
  T2              2               92
  T3              3               76
  T4              0               13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V5, binary
                  cls
clus                 0   1
  HNRNPL MUTATED     3   0
  HNRNPL WILD-TYPE 251   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HNRNPL MUTATED      3    0
  HNRNPL WILD-TYPE  251    4
   clus
vv  HNRNPL MUTATED HNRNPL WILD-TYPE
  0              3              251
  1              0                4
[1] 2 2
[1] FALSE
D67V6, binary
                  cls
clus                 0   1
  HNRNPL MUTATED     5   0
  HNRNPL WILD-TYPE 264   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HNRNPL MUTATED      5    0
  HNRNPL WILD-TYPE  264    4
   clus
vv  HNRNPL MUTATED HNRNPL WILD-TYPE
  0              5              264
  1              0                4
[1] 2 2
[1] FALSE
D67V7, binary
                  cls
clus                 0   1
  HNRNPL MUTATED     3   5
  HNRNPL WILD-TYPE 118 247
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HNRNPL MUTATED      3    5
  HNRNPL WILD-TYPE  118  247
        clus
vv       HNRNPL MUTATED HNRNPL WILD-TYPE
  FEMALE              3              118
  MALE                5              247
[1] 2 2
[1] FALSE
D67V8, binary
                  cls
clus                 0   1
  HNRNPL MUTATED     8   0
  HNRNPL WILD-TYPE 333   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HNRNPL MUTATED      8    0
  HNRNPL WILD-TYPE  333    9
     clus
vv    HNRNPL MUTATED HNRNPL WILD-TYPE
  NO               8              333
  YES              0                9
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  HNRNPL MUTATED                         0                        8
  HNRNPL WILD-TYPE                       3                      355
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  HNRNPL MUTATED                                  0
  HNRNPL WILD-TYPE                                7
D67V9, multiclass
                                  clus
vv                                 HNRNPL MUTATED HNRNPL WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                3
  HEPATOCELLULAR CARCINOMA                      8              355
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  HNRNPL MUTATED     7   1   0   0
  HNRNPL WILD-TYPE 320  15   1  22
D67V10, multiclass
    clus
vv   HNRNPL MUTATED HNRNPL WILD-TYPE
  R0              7              320
  R1              1               15
  R2              0                1
  RX              0               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HNRNPL MUTATED                                  0     3
  HNRNPL WILD-TYPE                                2   157
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HNRNPL MUTATED                           1     4
  HNRNPL WILD-TYPE                        16   180
D67V11, multiclass
                                  clus
vv                                 HNRNPL MUTATED HNRNPL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         3              157
  BLACK OR AFRICAN AMERICAN                     1               16
  WHITE                                         4              180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V12, binary
                  cls
clus                 0   1
  HNRNPL MUTATED     0   7
  HNRNPL WILD-TYPE  18 330
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HNRNPL MUTATED      0    7
  HNRNPL WILD-TYPE   18  330
                        clus
vv                       HNRNPL MUTATED HNRNPL WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              7              330
[1] 2 2
[1] FALSE

Clustering(68) Variable = FILIP1 MUTATION ANALYSIS
D68V1, survival
                  sevent
clus2                0   1
  FILIP1 MUTATED     5   8
  FILIP1 WILD-TYPE 232 122
  FILIP1 MUTATED FILIP1 WILD-TYPE 
              13              354 
  FILIP1 MUTATED FILIP1 WILD-TYPE 
               8              122 
$`FILIP1 MUTATED`
TCGA-BC-A110 TCGA-XR-A8TG TCGA-BW-A5NO TCGA-CC-5263 TCGA-CC-A7IL TCGA-DD-A1EE 
       69.57        29.52         0.66         4.24         9.14        11.47 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A4NR TCGA-DD-AAEE TCGA-FV-A2QQ 
       55.69         5.62        25.81         0.30        26.63        23.97 
TCGA-ZS-A9CG 
       11.21 

$`FILIP1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
        7.04        10.32        44.02         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
      120.82        40.41        56.91        49.84        47.74        18.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       20.81        22.92         1.18         8.55        13.02        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 
       10.59         0.66        17.10        14.76         1.51        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.38         1.12        44.42        45.93         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-CC-5258 TCGA-CC-5259 
       14.60        18.48        44.81        13.45         4.24         8.22 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT 
        2.86         3.19         3.39         3.35         7.20         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD 
        9.86         9.96        10.36        11.93        11.41         9.99 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II 
        8.94         7.13        21.34         9.83        12.00        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV 
       12.56         8.61         9.86         4.60        11.31         9.17 
TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        6.94         8.15        79.73        37.78        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
      113.00         7.33         2.60         0.46        21.76        51.29 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF 
       90.71        79.40        66.31        19.79        75.65        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       45.11        49.15         6.02        33.04        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
       21.14        27.19        19.76         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ 
       32.52        21.70        30.97        26.37        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        40.08        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        29.52        14.89        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       66.67        15.58        18.21        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 
       18.15        20.98        18.61        19.99         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       15.72        25.08        25.78        50.33        35.08        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       89.69        82.62        59.93        72.39        80.71        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        60.99 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        9.73         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
       19.10        27.88        12.03         0.03         0.33         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z 
       13.68        51.06        53.79        28.27        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        25.25        22.95 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       24.46        20.42        17.10        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        0.89        11.64         2.14        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       27.25        29.79        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       22.95        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       17.69        21.01         3.09         0.72         0.49         0.30 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.04        19.33        19.04        15.39        15.52        36.10 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       27.88        19.76        16.44         1.71        15.98        10.75 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       11.34         0.99        12.99        20.22        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        22.78        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.21        35.87        25.15        12.99        45.57        79.30 

  FILIP1 MUTATED FILIP1 WILD-TYPE 
            0.30             0.03 
  FILIP1 MUTATED FILIP1 WILD-TYPE 
           69.57           120.82 
  FILIP1 MUTATED FILIP1 WILD-TYPE 
          11.470           19.775 
[1] "0.3 - 69.6 (11.5)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "2.3"
D68V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  FILIP1 MUTATED         7        1         0          4          0          0
  FILIP1 WILD-TYPE     167       85         3         60          9          9
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  FILIP1 MUTATED          0         0         0
  FILIP1 WILD-TYPE        2         1         2
D68V3, multiclass
            clus
vv           FILIP1 MUTATED FILIP1 WILD-TYPE
  STAGE I                 7              167
  STAGE II                1               85
  STAGE III               0                3
  STAGE IIIA              4               60
  STAGE IIIB              0                9
  STAGE IIIC              0                9
  STAGE IV                0                2
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FILIP1 MUTATED     8   1   4   0
  FILIP1 WILD-TYPE 176  93  75  13
D68V4, multiclass
    clus
vv   FILIP1 MUTATED FILIP1 WILD-TYPE
  T1              8              176
  T2              1               93
  T3              4               75
  T4              0               13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V5, binary
                  cls
clus                 0   1
  FILIP1 MUTATED     6   0
  FILIP1 WILD-TYPE 248   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FILIP1 MUTATED      6    0
  FILIP1 WILD-TYPE  248    4
   clus
vv  FILIP1 MUTATED FILIP1 WILD-TYPE
  0              6              248
  1              0                4
[1] 2 2
[1] FALSE
D68V6, binary
                  cls
clus                 0   1
  FILIP1 MUTATED     9   0
  FILIP1 WILD-TYPE 260   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FILIP1 MUTATED      9    0
  FILIP1 WILD-TYPE  260    4
   clus
vv  FILIP1 MUTATED FILIP1 WILD-TYPE
  0              9              260
  1              0                4
[1] 2 2
[1] FALSE
D68V7, binary
                  cls
clus                 0   1
  FILIP1 MUTATED     3  10
  FILIP1 WILD-TYPE 118 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FILIP1 MUTATED      3   10
  FILIP1 WILD-TYPE  118  242
        clus
vv       FILIP1 MUTATED FILIP1 WILD-TYPE
  FEMALE              3              118
  MALE               10              242
[1] 2 2
[1] FALSE
D68V8, binary
                  cls
clus                 0   1
  FILIP1 MUTATED    12   1
  FILIP1 WILD-TYPE 329   8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FILIP1 MUTATED     12    1
  FILIP1 WILD-TYPE  329    8
     clus
vv    FILIP1 MUTATED FILIP1 WILD-TYPE
  NO              12              329
  YES              1                8
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  FILIP1 MUTATED                         0                       13
  FILIP1 WILD-TYPE                       3                      350
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  FILIP1 MUTATED                                  0
  FILIP1 WILD-TYPE                                7
D68V9, multiclass
                                  clus
vv                                 FILIP1 MUTATED FILIP1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                3
  HEPATOCELLULAR CARCINOMA                     13              350
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FILIP1 MUTATED    11   0   0   2
  FILIP1 WILD-TYPE 316  16   1  20
D68V10, multiclass
    clus
vv   FILIP1 MUTATED FILIP1 WILD-TYPE
  R0             11              316
  R1              0               16
  R2              0                1
  RX              2               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FILIP1 MUTATED                                  0     4
  FILIP1 WILD-TYPE                                2   156
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FILIP1 MUTATED                           2     7
  FILIP1 WILD-TYPE                        15   177
D68V11, multiclass
                                  clus
vv                                 FILIP1 MUTATED FILIP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         4              156
  BLACK OR AFRICAN AMERICAN                     2               15
  WHITE                                         7              177
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V12, binary
                  cls
clus                 0   1
  FILIP1 MUTATED     1  12
  FILIP1 WILD-TYPE  17 325
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FILIP1 MUTATED      1   12
  FILIP1 WILD-TYPE   17  325
                        clus
vv                       FILIP1 MUTATED FILIP1 WILD-TYPE
  HISPANIC OR LATINO                  1               17
  NOT HISPANIC OR LATINO             12              325
[1] 2 2
[1] FALSE

Clustering(69) Variable = FAM22F MUTATION ANALYSIS
D69V1, survival
                  sevent
clus2                0   1
  FAM22F MUTATED     1   3
  FAM22F WILD-TYPE 236 127
  FAM22F MUTATED FAM22F WILD-TYPE 
               4              363 
  FAM22F MUTATED FAM22F WILD-TYPE 
               3              127 
$`FAM22F MUTATED`
TCGA-CC-A3MA TCGA-DD-A119 TCGA-DD-A39X TCGA-G3-AAV3 
        9.96         7.33        55.69        13.55 

$`FAM22F WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB 
        4.24         3.35         7.20         3.32         9.86        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
       11.93        11.41         9.99         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        9.83        12.00        13.12        12.56         8.61         9.14 
TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.86         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A 
       79.73        37.78        83.57        53.33       113.00         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ 
       32.52        21.70        30.97        26.37        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       34.49        20.91         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
       14.33        66.67        15.58        18.21        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        89.69        82.62        59.93        72.39 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        60.99        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        20.61        19.59         0.62        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 
       14.40        60.89        23.97        19.10        27.88        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.03         0.33         0.39        13.68        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       28.27        14.86        21.53        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        25.25        22.95        24.46        20.42        17.10 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       14.70        20.78        11.87        14.14        15.78        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       11.80        12.23         0.89        11.64         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       58.88        26.27        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        22.78        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        25.71        23.21        35.87        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  FAM22F MUTATED FAM22F WILD-TYPE 
            7.33             0.03 
  FAM22F MUTATED FAM22F WILD-TYPE 
           55.69           120.82 
  FAM22F MUTATED FAM22F WILD-TYPE 
          11.755           19.790 
[1] "7.3 - 55.7 (11.8)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "2.6"
D69V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  FAM22F MUTATED         1        1         0          1          0          0
  FAM22F WILD-TYPE     173       85         3         63          9          9
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  FAM22F MUTATED          1         0         0
  FAM22F WILD-TYPE        1         1         2
D69V3, multiclass
            clus
vv           FAM22F MUTATED FAM22F WILD-TYPE
  STAGE I                 1              173
  STAGE II                1               85
  STAGE III               0                3
  STAGE IIIA              1               63
  STAGE IIIB              0                9
  STAGE IIIC              0                9
  STAGE IV                1                1
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAM22F MUTATED     1   1   2   0
  FAM22F WILD-TYPE 183  93  77  13
D69V4, multiclass
    clus
vv   FAM22F MUTATED FAM22F WILD-TYPE
  T1              1              183
  T2              1               93
  T3              2               77
  T4              0               13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V5, binary
                  cls
clus                 0   1
  FAM22F MUTATED     3   0
  FAM22F WILD-TYPE 251   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM22F MUTATED      3    0
  FAM22F WILD-TYPE  251    4
   clus
vv  FAM22F MUTATED FAM22F WILD-TYPE
  0              3              251
  1              0                4
[1] 2 2
[1] FALSE
D69V6, binary
                  cls
clus                 0   1
  FAM22F MUTATED     3   1
  FAM22F WILD-TYPE 266   3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM22F MUTATED      3    1
  FAM22F WILD-TYPE  266    3
   clus
vv  FAM22F MUTATED FAM22F WILD-TYPE
  0              3              266
  1              1                3
[1] 2 2
[1] FALSE
D69V7, binary
                  cls
clus                 0   1
  FAM22F MUTATED     2   2
  FAM22F WILD-TYPE 119 250
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM22F MUTATED      2    2
  FAM22F WILD-TYPE  119  250
        clus
vv       FAM22F MUTATED FAM22F WILD-TYPE
  FEMALE              2              119
  MALE                2              250
[1] 2 2
[1] FALSE
D69V8, binary
                  cls
clus                 0   1
  FAM22F MUTATED     3   0
  FAM22F WILD-TYPE 338   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM22F MUTATED      3    0
  FAM22F WILD-TYPE  338    9
     clus
vv    FAM22F MUTATED FAM22F WILD-TYPE
  NO               3              338
  YES              0                9
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  FAM22F MUTATED                         0                        4
  FAM22F WILD-TYPE                       3                      359
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  FAM22F MUTATED                                  0
  FAM22F WILD-TYPE                                7
D69V9, multiclass
                                  clus
vv                                 FAM22F MUTATED FAM22F WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                3
  HEPATOCELLULAR CARCINOMA                      4              359
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FAM22F MUTATED     3   0   1   0
  FAM22F WILD-TYPE 324  16   0  22
D69V10, multiclass
    clus
vv   FAM22F MUTATED FAM22F WILD-TYPE
  R0              3              324
  R1              0               16
  R2              1                0
  RX              0               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM22F MUTATED                                  0     2
  FAM22F WILD-TYPE                                2   158
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FAM22F MUTATED                           0     2
  FAM22F WILD-TYPE                        17   182
D69V11, multiclass
                                  clus
vv                                 FAM22F MUTATED FAM22F WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         2              158
  BLACK OR AFRICAN AMERICAN                     0               17
  WHITE                                         2              182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V12, binary
                  cls
clus                 0   1
  FAM22F MUTATED     0   4
  FAM22F WILD-TYPE  18 333
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM22F MUTATED      0    4
  FAM22F WILD-TYPE   18  333
                        clus
vv                       FAM22F MUTATED FAM22F WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              4              333
[1] 2 2
[1] FALSE

Clustering(70) Variable = GPSM2 MUTATION ANALYSIS
D70V1, survival
                 sevent
clus2               0   1
  GPSM2 MUTATED     1   3
  GPSM2 WILD-TYPE 236 127
  GPSM2 MUTATED GPSM2 WILD-TYPE 
              4             363 
  GPSM2 MUTATED GPSM2 WILD-TYPE 
              3             127 
$`GPSM2 MUTATED`
TCGA-BC-A112 TCGA-BC-A3KF TCGA-DD-A39X TCGA-FV-A2QR 
        5.03         0.26        55.69        19.10 

$`GPSM2 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        20.81        22.92         1.18         8.55        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        17.10        14.76         1.51 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
       25.32        23.38         1.12        44.42        45.93        22.36 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       14.60        18.48        44.81        13.45         0.66         4.24 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
        8.22         2.86         3.19         3.39         4.24         3.35 
TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        7.20         3.32         9.86         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS 
       12.00        13.12        12.56         8.61         9.14         9.86 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ 
       32.52        21.70        30.97        26.37        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       34.49        20.91         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
       14.33        66.67        15.58        18.21        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        89.69        82.62        59.93        72.39 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        60.99        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        20.61        19.59         0.62        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       14.40        60.89        23.97        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       25.25        22.95        24.46        20.42        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       20.78        11.87        14.14        15.78        15.65        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       12.23        13.55         0.89        11.64         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       58.88        26.27        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        22.78        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        25.71        23.21        35.87        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  GPSM2 MUTATED GPSM2 WILD-TYPE 
           0.26            0.03 
  GPSM2 MUTATED GPSM2 WILD-TYPE 
          55.69          120.82 
  GPSM2 MUTATED GPSM2 WILD-TYPE 
         12.065          19.790 
[1] "0.3 - 55.7 (12.1)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "2.9"
D70V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  GPSM2 MUTATED         3        0         0          0          0          0
  GPSM2 WILD-TYPE     171       86         3         64          9          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  GPSM2 MUTATED          0         0         0
  GPSM2 WILD-TYPE        2         1         2
D70V3, multiclass
            clus
vv           GPSM2 MUTATED GPSM2 WILD-TYPE
  STAGE I                3             171
  STAGE II               0              86
  STAGE III              0               3
  STAGE IIIA             0              64
  STAGE IIIB             0               9
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GPSM2 MUTATED     3   0   1   0
  GPSM2 WILD-TYPE 181  94  78  13
D70V4, multiclass
    clus
vv   GPSM2 MUTATED GPSM2 WILD-TYPE
  T1             3             181
  T2             0              94
  T3             1              78
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V5, binary
                 cls
clus                0   1
  GPSM2 MUTATED     1   0
  GPSM2 WILD-TYPE 253   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM2 MUTATED      1    0
  GPSM2 WILD-TYPE  253    4
   clus
vv  GPSM2 MUTATED GPSM2 WILD-TYPE
  0             1             253
  1             0               4
[1] 2 2
[1] FALSE
D70V6, binary
                 cls
clus                0   1
  GPSM2 MUTATED     3   0
  GPSM2 WILD-TYPE 266   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM2 MUTATED      3    0
  GPSM2 WILD-TYPE  266    4
   clus
vv  GPSM2 MUTATED GPSM2 WILD-TYPE
  0             3             266
  1             0               4
[1] 2 2
[1] FALSE
D70V7, binary
                 cls
clus                0   1
  GPSM2 MUTATED     2   2
  GPSM2 WILD-TYPE 119 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM2 MUTATED      2    2
  GPSM2 WILD-TYPE  119  250
        clus
vv       GPSM2 MUTATED GPSM2 WILD-TYPE
  FEMALE             2             119
  MALE               2             250
[1] 2 2
[1] FALSE
D70V8, binary
                 cls
clus                0   1
  GPSM2 MUTATED     3   0
  GPSM2 WILD-TYPE 338   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM2 MUTATED      3    0
  GPSM2 WILD-TYPE  338    9
     clus
vv    GPSM2 MUTATED GPSM2 WILD-TYPE
  NO              3             338
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  GPSM2 MUTATED                         0                        4
  GPSM2 WILD-TYPE                       3                      359
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  GPSM2 MUTATED                                  0
  GPSM2 WILD-TYPE                                7
D70V9, multiclass
                                  clus
vv                                 GPSM2 MUTATED GPSM2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                     4             359
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GPSM2 MUTATED     3   0   0   1
  GPSM2 WILD-TYPE 324  16   1  21
D70V10, multiclass
    clus
vv   GPSM2 MUTATED GPSM2 WILD-TYPE
  R0             3             324
  R1             0              16
  R2             0               1
  RX             1              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPSM2 MUTATED                                  0     0
  GPSM2 WILD-TYPE                                2   160
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GPSM2 MUTATED                           0     4
  GPSM2 WILD-TYPE                        17   180
D70V11, multiclass
                                  clus
vv                                 GPSM2 MUTATED GPSM2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0             160
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        4             180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V12, binary
                 cls
clus                0   1
  GPSM2 MUTATED     0   3
  GPSM2 WILD-TYPE  18 334
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM2 MUTATED      0    3
  GPSM2 WILD-TYPE   18  334
                        clus
vv                       GPSM2 MUTATED GPSM2 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             3             334
[1] 2 2
[1] FALSE

Clustering(71) Variable = RCCD1 MUTATION ANALYSIS
D71V1, survival
                 sevent
clus2               0   1
  RCCD1 MUTATED     2   3
  RCCD1 WILD-TYPE 235 127
  RCCD1 MUTATED RCCD1 WILD-TYPE 
              5             362 
  RCCD1 MUTATED RCCD1 WILD-TYPE 
              3             127 
$`RCCD1 MUTATED`
TCGA-DD-AAEA TCGA-CC-A3MB TCGA-DD-A1EG TCGA-DD-A3A0 TCGA-DD-AADB 
       18.90        10.36        45.11        25.81        40.83 

$`RCCD1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.17        21.83        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        20.81        22.92         1.18         8.55        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        17.10        14.76         1.51 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        14.60        18.48        44.81        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.24         8.22         2.86         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC 
        3.35         7.20         3.32         9.86         9.96        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS 
       12.00        13.12        12.56         8.61         9.14         9.86 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        11.47        12.95        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
        5.62        19.76         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       21.70        30.97        26.37        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       22.09        40.08        40.54        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
        0.39        29.52        14.89        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       25.08        26.63        25.78        50.33        35.08        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       89.69        82.62        59.93        72.39        80.71        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        60.99 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        9.73         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.39        13.68        51.06        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
       22.95        24.46        20.42        17.10        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       11.87        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  RCCD1 MUTATED RCCD1 WILD-TYPE 
          10.36            0.03 
  RCCD1 MUTATED RCCD1 WILD-TYPE 
          45.11          120.82 
  RCCD1 MUTATED RCCD1 WILD-TYPE 
          25.81           19.76 
[1] "10.4 - 45.1 (25.8)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1.6"
D71V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  RCCD1 MUTATED         4        0         0          1          0          0
  RCCD1 WILD-TYPE     170       86         3         63          9          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  RCCD1 MUTATED          0         0         0
  RCCD1 WILD-TYPE        2         1         2
D71V3, multiclass
            clus
vv           RCCD1 MUTATED RCCD1 WILD-TYPE
  STAGE I                4             170
  STAGE II               0              86
  STAGE III              0               3
  STAGE IIIA             1              63
  STAGE IIIB             0               9
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RCCD1 MUTATED     4   0   1   0
  RCCD1 WILD-TYPE 180  94  78  13
D71V4, multiclass
    clus
vv   RCCD1 MUTATED RCCD1 WILD-TYPE
  T1             4             180
  T2             0              94
  T3             1              78
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V5, binary
                 cls
clus                0   1
  RCCD1 MUTATED     4   0
  RCCD1 WILD-TYPE 250   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCCD1 MUTATED      4    0
  RCCD1 WILD-TYPE  250    4
   clus
vv  RCCD1 MUTATED RCCD1 WILD-TYPE
  0             4             250
  1             0               4
[1] 2 2
[1] FALSE
D71V6, binary
                 cls
clus                0   1
  RCCD1 MUTATED     5   0
  RCCD1 WILD-TYPE 264   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCCD1 MUTATED      5    0
  RCCD1 WILD-TYPE  264    4
   clus
vv  RCCD1 MUTATED RCCD1 WILD-TYPE
  0             5             264
  1             0               4
[1] 2 2
[1] FALSE
D71V7, binary
                 cls
clus                0   1
  RCCD1 MUTATED     0   5
  RCCD1 WILD-TYPE 121 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCCD1 MUTATED      0    5
  RCCD1 WILD-TYPE  121  247
        clus
vv       RCCD1 MUTATED RCCD1 WILD-TYPE
  FEMALE             0             121
  MALE               5             247
[1] 2 2
[1] FALSE
D71V8, binary
                 cls
clus                0   1
  RCCD1 MUTATED     5   0
  RCCD1 WILD-TYPE 336   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCCD1 MUTATED      5    0
  RCCD1 WILD-TYPE  336    9
     clus
vv    RCCD1 MUTATED RCCD1 WILD-TYPE
  NO              5             336
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  RCCD1 MUTATED                         0                        5
  RCCD1 WILD-TYPE                       3                      358
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  RCCD1 MUTATED                                  0
  RCCD1 WILD-TYPE                                7
D71V9, multiclass
                                  clus
vv                                 RCCD1 MUTATED RCCD1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                     5             358
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RCCD1 MUTATED     5   0   0   0
  RCCD1 WILD-TYPE 322  16   1  22
D71V10, multiclass
    clus
vv   RCCD1 MUTATED RCCD1 WILD-TYPE
  R0             5             322
  R1             0              16
  R2             0               1
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RCCD1 MUTATED                                  0     3
  RCCD1 WILD-TYPE                                2   157
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RCCD1 MUTATED                           0     2
  RCCD1 WILD-TYPE                        17   182
D71V11, multiclass
                                  clus
vv                                 RCCD1 MUTATED RCCD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        3             157
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        2             182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V12, binary
                 cls
clus                0   1
  RCCD1 MUTATED     0   5
  RCCD1 WILD-TYPE  18 332
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCCD1 MUTATED      0    5
  RCCD1 WILD-TYPE   18  332
                        clus
vv                       RCCD1 MUTATED RCCD1 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             5             332
[1] 2 2
[1] FALSE

Clustering(72) Variable = PTGR1 MUTATION ANALYSIS
D72V1, survival
                 sevent
clus2               0   1
  PTGR1 MUTATED     3   2
  PTGR1 WILD-TYPE 234 128
  PTGR1 MUTATED PTGR1 WILD-TYPE 
              5             362 
  PTGR1 MUTATED PTGR1 WILD-TYPE 
              2             128 
$`PTGR1 MUTATED`
TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-AADB TCGA-G3-A3CK TCGA-G3-A7M7 
        5.62        25.81        40.83        19.23        11.87 

$`PTGR1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       21.34         9.83        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
        9.14         9.86         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.15        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65        11.47        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       45.11        49.15         6.02        33.04        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       21.14        27.19        55.69        19.76         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       33.14        32.52        21.70        30.97        26.37        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       23.05        22.78         1.45        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        75.65        76.41        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       71.80        12.00        15.42         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
        0.30         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       14.20        59.31        51.35        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADC 
       42.58        44.22        22.09        40.08        40.54        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       34.49        20.91         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
       14.33        66.67        15.58        18.21        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        89.69        82.62        59.93        72.39 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        60.99        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        20.61        19.59         0.62        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 
       14.40        60.89        23.97        19.10        27.88        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.03         0.33         0.39        13.68        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       28.27        14.86        21.53        25.64         5.92        19.53 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       25.25        22.95        24.46        20.42        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       20.78        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  PTGR1 MUTATED PTGR1 WILD-TYPE 
           5.62            0.03 
  PTGR1 MUTATED PTGR1 WILD-TYPE 
          40.83          120.82 
  PTGR1 MUTATED PTGR1 WILD-TYPE 
         19.230          19.775 
[1] "5.6 - 40.8 (19.2)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.4"
D72V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PTGR1 MUTATED         5        0         0          0          0          0
  PTGR1 WILD-TYPE     169       86         3         64          9          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  PTGR1 MUTATED          0         0         0
  PTGR1 WILD-TYPE        2         1         2
D72V3, multiclass
            clus
vv           PTGR1 MUTATED PTGR1 WILD-TYPE
  STAGE I                5             169
  STAGE II               0              86
  STAGE III              0               3
  STAGE IIIA             0              64
  STAGE IIIB             0               9
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTGR1 MUTATED     5   0   0   0
  PTGR1 WILD-TYPE 179  94  79  13
D72V4, multiclass
    clus
vv   PTGR1 MUTATED PTGR1 WILD-TYPE
  T1             5             179
  T2             0              94
  T3             0              79
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V5, binary
                 cls
clus                0   1
  PTGR1 MUTATED     2   0
  PTGR1 WILD-TYPE 252   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTGR1 MUTATED      2    0
  PTGR1 WILD-TYPE  252    4
   clus
vv  PTGR1 MUTATED PTGR1 WILD-TYPE
  0             2             252
  1             0               4
[1] 2 2
[1] FALSE
D72V6, binary
                 cls
clus                0   1
  PTGR1 MUTATED     4   0
  PTGR1 WILD-TYPE 265   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTGR1 MUTATED      4    0
  PTGR1 WILD-TYPE  265    4
   clus
vv  PTGR1 MUTATED PTGR1 WILD-TYPE
  0             4             265
  1             0               4
[1] 2 2
[1] FALSE
D72V7, binary
                 cls
clus                0   1
  PTGR1 MUTATED     0   5
  PTGR1 WILD-TYPE 121 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTGR1 MUTATED      0    5
  PTGR1 WILD-TYPE  121  247
        clus
vv       PTGR1 MUTATED PTGR1 WILD-TYPE
  FEMALE             0             121
  MALE               5             247
[1] 2 2
[1] FALSE
D72V8, binary
                 cls
clus                0   1
  PTGR1 MUTATED     5   0
  PTGR1 WILD-TYPE 336   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTGR1 MUTATED      5    0
  PTGR1 WILD-TYPE  336    9
     clus
vv    PTGR1 MUTATED PTGR1 WILD-TYPE
  NO              5             336
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  PTGR1 MUTATED                         0                        5
  PTGR1 WILD-TYPE                       3                      358
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  PTGR1 MUTATED                                  0
  PTGR1 WILD-TYPE                                7
D72V9, multiclass
                                  clus
vv                                 PTGR1 MUTATED PTGR1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                     5             358
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PTGR1 MUTATED     5   0   0   0
  PTGR1 WILD-TYPE 322  16   1  22
D72V10, multiclass
    clus
vv   PTGR1 MUTATED PTGR1 WILD-TYPE
  R0             5             322
  R1             0              16
  R2             0               1
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTGR1 MUTATED                                  0     3
  PTGR1 WILD-TYPE                                2   157
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTGR1 MUTATED                           0     2
  PTGR1 WILD-TYPE                        17   182
D72V11, multiclass
                                  clus
vv                                 PTGR1 MUTATED PTGR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        3             157
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        2             182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V12, binary
                 cls
clus                0   1
  PTGR1 MUTATED     0   5
  PTGR1 WILD-TYPE  18 332
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTGR1 MUTATED      0    5
  PTGR1 WILD-TYPE   18  332
                        clus
vv                       PTGR1 MUTATED PTGR1 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             5             332
[1] 2 2
[1] FALSE

Clustering(73) Variable = SAMM50 MUTATION ANALYSIS
D73V1, survival
                  sevent
clus2                0   1
  SAMM50 MUTATED     1   2
  SAMM50 WILD-TYPE 236 128
  SAMM50 MUTATED SAMM50 WILD-TYPE 
               3              364 
  SAMM50 MUTATED SAMM50 WILD-TYPE 
               2              128 
$`SAMM50 MUTATED`
TCGA-DD-A1EG TCGA-DD-A39Y TCGA-G3-A3CJ 
       45.11         5.62        19.53 

$`SAMM50 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       21.34         9.83        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
        9.14         9.86         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.15        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65        11.47        12.95 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       27.19        55.69        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       33.14        32.52        21.70        30.97        26.37        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       23.05        22.78         1.45        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        75.65        76.41        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       71.80        12.00        15.42         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
        0.30         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       14.20        59.31        51.35        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.05        34.49        20.91         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        23.74        15.72        25.08        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        90.48        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.39        80.71        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        60.99        53.69        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       28.08        13.91        13.35         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20        14.04        13.15        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        20.61        19.59         0.62 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        14.86        21.53        25.64         5.92 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        25.25        22.95        24.46        20.42        17.10 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       14.70        20.78        11.87        14.14        15.78        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80        12.23        13.55         0.89        11.64         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        28.90         1.02         2.20         2.99        37.71 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06        16.83        11.80        27.25        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        26.27        17.69        21.01         3.09 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        15.52        36.10        27.88        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        1.71        15.98        10.75        11.34         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       20.22        24.85        18.28        33.86        30.41        22.78 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       13.55        35.77        25.71        23.21        35.87        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        79.30        11.21 

  SAMM50 MUTATED SAMM50 WILD-TYPE 
            5.62             0.03 
  SAMM50 MUTATED SAMM50 WILD-TYPE 
           45.11           120.82 
  SAMM50 MUTATED SAMM50 WILD-TYPE 
          19.530           19.775 
[1] "5.6 - 45.1 (19.5)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "2.2"
D73V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  SAMM50 MUTATED         2        1         0          0          0          0
  SAMM50 WILD-TYPE     172       85         3         64          9          9
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  SAMM50 MUTATED          0         0         0
  SAMM50 WILD-TYPE        2         1         2
D73V3, multiclass
            clus
vv           SAMM50 MUTATED SAMM50 WILD-TYPE
  STAGE I                 2              172
  STAGE II                1               85
  STAGE III               0                3
  STAGE IIIA              0               64
  STAGE IIIB              0                9
  STAGE IIIC              0                9
  STAGE IV                0                2
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SAMM50 MUTATED     2   1   0   0
  SAMM50 WILD-TYPE 182  93  79  13
D73V4, multiclass
    clus
vv   SAMM50 MUTATED SAMM50 WILD-TYPE
  T1              2              182
  T2              1               93
  T3              0               79
  T4              0               13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V5, binary
                  cls
clus                 0   1
  SAMM50 MUTATED     2   0
  SAMM50 WILD-TYPE 252   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMM50 MUTATED      2    0
  SAMM50 WILD-TYPE  252    4
   clus
vv  SAMM50 MUTATED SAMM50 WILD-TYPE
  0              2              252
  1              0                4
[1] 2 2
[1] FALSE
D73V6, binary
                  cls
clus                 0   1
  SAMM50 MUTATED     3   0
  SAMM50 WILD-TYPE 266   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMM50 MUTATED      3    0
  SAMM50 WILD-TYPE  266    4
   clus
vv  SAMM50 MUTATED SAMM50 WILD-TYPE
  0              3              266
  1              0                4
[1] 2 2
[1] FALSE
D73V7, binary
                  cls
clus                 0   1
  SAMM50 MUTATED     0   3
  SAMM50 WILD-TYPE 121 249
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMM50 MUTATED      0    3
  SAMM50 WILD-TYPE  121  249
        clus
vv       SAMM50 MUTATED SAMM50 WILD-TYPE
  FEMALE              0              121
  MALE                3              249
[1] 2 2
[1] FALSE
D73V8, binary
                  cls
clus                 0   1
  SAMM50 MUTATED     3   0
  SAMM50 WILD-TYPE 338   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMM50 MUTATED      3    0
  SAMM50 WILD-TYPE  338    9
     clus
vv    SAMM50 MUTATED SAMM50 WILD-TYPE
  NO               3              338
  YES              0                9
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  SAMM50 MUTATED                         0                        3
  SAMM50 WILD-TYPE                       3                      360
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  SAMM50 MUTATED                                  0
  SAMM50 WILD-TYPE                                7
D73V9, multiclass
                                  clus
vv                                 SAMM50 MUTATED SAMM50 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                3
  HEPATOCELLULAR CARCINOMA                      3              360
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SAMM50 MUTATED     3   0   0   0
  SAMM50 WILD-TYPE 324  16   1  22
D73V10, multiclass
    clus
vv   SAMM50 MUTATED SAMM50 WILD-TYPE
  R0              3              324
  R1              0               16
  R2              0                1
  RX              0               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SAMM50 MUTATED                                  1     1
  SAMM50 WILD-TYPE                                1   159
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SAMM50 MUTATED                           0     1
  SAMM50 WILD-TYPE                        17   183
D73V11, multiclass
                                  clus
vv                                 SAMM50 MUTATED SAMM50 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                1
  ASIAN                                         1              159
  BLACK OR AFRICAN AMERICAN                     0               17
  WHITE                                         1              183
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V12, binary
                  cls
clus                 0   1
  SAMM50 MUTATED     0   3
  SAMM50 WILD-TYPE  18 334
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMM50 MUTATED      0    3
  SAMM50 WILD-TYPE   18  334
                        clus
vv                       SAMM50 MUTATED SAMM50 WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              3              334
[1] 2 2
[1] FALSE

Clustering(74) Variable = PBRM1 MUTATION ANALYSIS
D74V1, survival
                 sevent
clus2               0   1
  PBRM1 MUTATED     6   3
  PBRM1 WILD-TYPE 231 127
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              9             358 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              3             127 
$`PBRM1 MUTATED`
TCGA-G3-A6UC TCGA-DD-A116 TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A3A0 TCGA-DD-AADP 
       22.06        53.33        79.40        11.47        25.81        15.06 
TCGA-DD-AADY TCGA-FV-A3I0 TCGA-LG-A9QC 
       18.25        27.88        13.97 

$`PBRM1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A7M9 
        8.12         6.38        81.73        30.74        22.13         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        20.81        22.92         1.18         8.55        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        17.10        14.76         1.51 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        14.60        18.48        44.81        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.24         8.22         2.86         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.35         7.20         3.32         9.86         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
       11.93        11.41         9.99         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        9.83        12.00        13.12        12.56         8.61         9.14 
TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.86         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       79.73        37.78        83.57       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        21.76        51.29        90.71        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        12.95        45.11        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y 
       18.35        13.64        21.14        27.19        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.76         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE 
      107.11        13.78        30.61        33.14        32.52        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        26.37        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       35.67       114.35        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       76.41        55.40        12.53        71.80        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       42.81        61.68        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
        0.39        29.52        14.89        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       18.21        19.30        18.25        18.15        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       19.99         4.64        23.74        15.72        25.08        26.63 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       25.78        50.33        35.08        90.48        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       59.93        72.39        80.71        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        60.99        53.69        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       26.93        28.08        13.91        13.35         9.73         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
       12.82         0.20        14.04        13.15        13.41        13.35 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        1.84         0.20        18.74        19.99        20.61        19.59 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        0.62        11.93        14.40        60.89        23.97        19.10 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       19.53        19.23        25.25        22.95        24.46        20.42 
TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       17.10        14.70        20.78        11.87        14.14        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.65        11.80        12.23        13.55         0.89        11.64 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 
       37.71        17.06        16.83        11.80        27.25        29.79 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        26.27        17.69        21.01         3.09 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        15.52        36.10        27.88        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        1.71        15.98        10.75        11.34         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       20.22        24.85        18.28        33.86        30.41        22.78 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       13.55        35.77        25.71        23.21        35.87        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        79.30        11.21 

  PBRM1 MUTATED PBRM1 WILD-TYPE 
          11.47            0.03 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
          79.40          120.82 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
          22.06           19.76 
[1] "11.5 - 79.4 (22.1)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1.2"
D74V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PBRM1 MUTATED         4        2         0          2          1          0
  PBRM1 WILD-TYPE     170       84         3         62          8          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  PBRM1 MUTATED          0         0         0
  PBRM1 WILD-TYPE        2         1         2
D74V3, multiclass
            clus
vv           PBRM1 MUTATED PBRM1 WILD-TYPE
  STAGE I                4             170
  STAGE II               2              84
  STAGE III              0               3
  STAGE IIIA             2              62
  STAGE IIIB             1               8
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PBRM1 MUTATED     4   2   3   0
  PBRM1 WILD-TYPE 180  92  76  13
D74V4, multiclass
    clus
vv   PBRM1 MUTATED PBRM1 WILD-TYPE
  T1             4             180
  T2             2              92
  T3             3              76
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V5, binary
                 cls
clus                0   1
  PBRM1 MUTATED     6   0
  PBRM1 WILD-TYPE 248   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      6    0
  PBRM1 WILD-TYPE  248    4
   clus
vv  PBRM1 MUTATED PBRM1 WILD-TYPE
  0             6             248
  1             0               4
[1] 2 2
[1] FALSE
D74V6, binary
                 cls
clus                0   1
  PBRM1 MUTATED     9   0
  PBRM1 WILD-TYPE 260   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      9    0
  PBRM1 WILD-TYPE  260    4
   clus
vv  PBRM1 MUTATED PBRM1 WILD-TYPE
  0             9             260
  1             0               4
[1] 2 2
[1] FALSE
D74V7, binary
                 cls
clus                0   1
  PBRM1 MUTATED     2   7
  PBRM1 WILD-TYPE 119 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      2    7
  PBRM1 WILD-TYPE  119  245
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  FEMALE             2             119
  MALE               7             245
[1] 2 2
[1] FALSE
D74V8, binary
                 cls
clus                0   1
  PBRM1 MUTATED     8   1
  PBRM1 WILD-TYPE 333   8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      8    1
  PBRM1 WILD-TYPE  333    8
     clus
vv    PBRM1 MUTATED PBRM1 WILD-TYPE
  NO              8             333
  YES             1               8
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  PBRM1 MUTATED                         0                        8
  PBRM1 WILD-TYPE                       3                      355
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  PBRM1 MUTATED                                  1
  PBRM1 WILD-TYPE                                6
D74V9, multiclass
                                  clus
vv                                 PBRM1 MUTATED PBRM1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                     8             355
  HEPATOCHOLANGIOCARCINOMA (MIXED)             1               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PBRM1 MUTATED     9   0   0   0
  PBRM1 WILD-TYPE 318  16   1  22
D74V10, multiclass
    clus
vv   PBRM1 MUTATED PBRM1 WILD-TYPE
  R0             9             318
  R1             0              16
  R2             0               1
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PBRM1 MUTATED                                  0     4
  PBRM1 WILD-TYPE                                2   156
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PBRM1 MUTATED                           0     5
  PBRM1 WILD-TYPE                        17   179
D74V11, multiclass
                                  clus
vv                                 PBRM1 MUTATED PBRM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        4             156
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        5             179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V12, binary
                 cls
clus                0   1
  PBRM1 MUTATED     0   9
  PBRM1 WILD-TYPE  18 328
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      0    9
  PBRM1 WILD-TYPE   18  328
                        clus
vv                       PBRM1 MUTATED PBRM1 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             9             328
[1] 2 2
[1] FALSE

Clustering(75) Variable = SGK269 MUTATION ANALYSIS
D75V1, survival
                  sevent
clus2                0   1
  SGK269 MUTATED     3   4
  SGK269 WILD-TYPE 234 126
  SGK269 MUTATED SGK269 WILD-TYPE 
               7              360 
  SGK269 MUTATED SGK269 WILD-TYPE 
               4              126 
$`SGK269 MUTATED`
TCGA-4R-AA8I TCGA-BC-A3KG TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A39Z 
        8.61        22.36        79.40        11.47        45.11        19.76 
TCGA-ED-A7XO 
       14.04 

$`SGK269 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        11.74        38.40        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        20.81        22.92         1.18         8.55        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        17.10        14.76         1.51 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       14.60        18.48        44.81        13.45         0.66         4.24 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
        8.22         2.86         3.19         3.39         4.24         3.35 
TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        7.20         3.32         9.86         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS 
       12.00        13.12        12.56         8.61         9.14         9.86 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        21.76        51.29        90.71        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       75.65        12.95        49.15         6.02        33.04        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 
       13.64        21.14        27.19        55.69         5.62        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF 
       13.78        30.61        33.14        32.52        21.70        30.97 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       26.37        30.15        30.51        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      114.35        13.48         0.53        11.41        75.65        76.41 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        71.80        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
       53.19        69.11         0.30         3.52        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
       61.68        13.64        14.20        59.31        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       50.33        46.82         5.59        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       40.54        40.83        13.97        40.47        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       37.64        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       29.52        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.21        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
       18.61        19.99         4.64        23.74        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       26.63        25.78        50.33        35.08        90.48        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       82.62        59.93        72.39        80.71        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       64.77        62.47        66.25        65.39        60.99        53.69 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       29.92        26.93        28.08        13.91        13.35         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
        0.20        12.82         0.20        13.15        13.41        13.35 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        1.84         0.20        18.74        19.99        20.61        19.59 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        0.62        11.93        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S 
       27.88        12.03         0.03         0.33         0.39        13.68 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       51.06        53.79        28.27        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
        5.92        19.53        19.23        25.25        22.95        24.46 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 
       20.42        17.10        14.70        20.78        11.87        14.14 
TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 
       15.78        15.65        11.80        12.23        13.55         0.89 
TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB 
       11.64         2.14        11.87        28.90         1.02         2.20 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 
        2.99        37.71        17.06        16.83        11.80        27.25 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       29.79        13.97        12.03         9.57        16.67        22.95 
TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V 
       20.71         7.53        10.85        58.88        26.27        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 
       21.01         3.09         0.72         0.49         0.30        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       19.33        19.04        15.39        15.52        36.10        27.88 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L 
       19.76        16.44         1.71        15.98        10.75        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD 
        0.99        12.99        20.22        24.85        18.28        33.86 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       30.41        22.78        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.87        25.15        12.99        45.57        79.30        11.21 

  SGK269 MUTATED SGK269 WILD-TYPE 
            8.61             0.03 
  SGK269 MUTATED SGK269 WILD-TYPE 
           79.40           120.82 
  SGK269 MUTATED SGK269 WILD-TYPE 
          19.760           19.775 
[1] "8.6 - 79.4 (19.8)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.6"
D75V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  SGK269 MUTATED         2        4         0          2          0          0
  SGK269 WILD-TYPE     172       82         3         62          9          9
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  SGK269 MUTATED          0         0         0
  SGK269 WILD-TYPE        2         1         2
D75V3, multiclass
            clus
vv           SGK269 MUTATED SGK269 WILD-TYPE
  STAGE I                 2              172
  STAGE II                4               82
  STAGE III               0                3
  STAGE IIIA              2               62
  STAGE IIIB              0                9
  STAGE IIIC              0                9
  STAGE IV                0                2
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SGK269 MUTATED     2   4   2   0
  SGK269 WILD-TYPE 182  90  77  13
D75V4, multiclass
    clus
vv   SGK269 MUTATED SGK269 WILD-TYPE
  T1              2              182
  T2              4               90
  T3              2               77
  T4              0               13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V5, binary
                  cls
clus                 0   1
  SGK269 MUTATED     5   0
  SGK269 WILD-TYPE 249   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SGK269 MUTATED      5    0
  SGK269 WILD-TYPE  249    4
   clus
vv  SGK269 MUTATED SGK269 WILD-TYPE
  0              5              249
  1              0                4
[1] 2 2
[1] FALSE
D75V6, binary
                  cls
clus                 0   1
  SGK269 MUTATED     6   0
  SGK269 WILD-TYPE 263   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SGK269 MUTATED      6    0
  SGK269 WILD-TYPE  263    4
   clus
vv  SGK269 MUTATED SGK269 WILD-TYPE
  0              6              263
  1              0                4
[1] 2 2
[1] FALSE
D75V7, binary
                  cls
clus                 0   1
  SGK269 MUTATED     2   6
  SGK269 WILD-TYPE 119 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SGK269 MUTATED      2    6
  SGK269 WILD-TYPE  119  246
        clus
vv       SGK269 MUTATED SGK269 WILD-TYPE
  FEMALE              2              119
  MALE                6              246
[1] 2 2
[1] FALSE
D75V8, binary
                  cls
clus                 0   1
  SGK269 MUTATED     6   0
  SGK269 WILD-TYPE 335   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SGK269 MUTATED      6    0
  SGK269 WILD-TYPE  335    9
     clus
vv    SGK269 MUTATED SGK269 WILD-TYPE
  NO               6              335
  YES              0                9
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  SGK269 MUTATED                         0                        8
  SGK269 WILD-TYPE                       3                      355
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  SGK269 MUTATED                                  0
  SGK269 WILD-TYPE                                7
D75V9, multiclass
                                  clus
vv                                 SGK269 MUTATED SGK269 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                3
  HEPATOCELLULAR CARCINOMA                      8              355
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SGK269 MUTATED     7   0   0   1
  SGK269 WILD-TYPE 320  16   1  21
D75V10, multiclass
    clus
vv   SGK269 MUTATED SGK269 WILD-TYPE
  R0              7              320
  R1              0               16
  R2              0                1
  RX              1               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SGK269 MUTATED                                  0     2
  SGK269 WILD-TYPE                                2   158
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SGK269 MUTATED                           0     5
  SGK269 WILD-TYPE                        17   179
D75V11, multiclass
                                  clus
vv                                 SGK269 MUTATED SGK269 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         2              158
  BLACK OR AFRICAN AMERICAN                     0               17
  WHITE                                         5              179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V12, binary
                  cls
clus                 0   1
  SGK269 MUTATED     0   7
  SGK269 WILD-TYPE  18 330
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SGK269 MUTATED      0    7
  SGK269 WILD-TYPE   18  330
                        clus
vv                       SGK269 MUTATED SGK269 WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              7              330
[1] 2 2
[1] FALSE

Clustering(76) Variable = LEO1 MUTATION ANALYSIS
D76V1, survival
                sevent
clus2              0   1
  LEO1 MUTATED     1   4
  LEO1 WILD-TYPE 236 126
  LEO1 MUTATED LEO1 WILD-TYPE 
             5            362 
  LEO1 MUTATED LEO1 WILD-TYPE 
             4            126 
$`LEO1 MUTATED`
TCGA-CC-5258 TCGA-DD-A116 TCGA-DD-A1EE TCGA-DD-AACI TCGA-DD-AADM 
        4.24        53.33        11.47        53.19         0.39 

$`LEO1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.66         8.22         2.86         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.35         7.20         3.32         9.86         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
       11.93        11.41         9.99         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        9.83        12.00        13.12        12.56         8.61         9.14 
TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.86         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       79.73        37.78        83.57       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ 
       32.52        21.70        30.97        26.37        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       12.00        15.42         6.41        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        40.08        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
       20.91        29.52        14.89        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       25.08        26.63        25.78        50.33        35.08        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       89.69        82.62        59.93        72.39        80.71        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        60.99 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        9.73         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.39        13.68        51.06        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
       22.95        24.46        20.42        17.10        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       11.87        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  LEO1 MUTATED LEO1 WILD-TYPE 
          0.39           0.03 
  LEO1 MUTATED LEO1 WILD-TYPE 
         53.33         120.82 
  LEO1 MUTATED LEO1 WILD-TYPE 
        11.470         19.775 
[1] "0.4 - 53.3 (11.5)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "2.8"
D76V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  LEO1 MUTATED         0        3         0          2          0          0
  LEO1 WILD-TYPE     174       83         3         62          9          9
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  LEO1 MUTATED          0         0         0
  LEO1 WILD-TYPE        2         1         2
D76V3, multiclass
            clus
vv           LEO1 MUTATED LEO1 WILD-TYPE
  STAGE I               0            174
  STAGE II              3             83
  STAGE III             0              3
  STAGE IIIA            2             62
  STAGE IIIB            0              9
  STAGE IIIC            0              9
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LEO1 MUTATED     0   3   2   0
  LEO1 WILD-TYPE 184  91  77  13
D76V4, multiclass
    clus
vv   LEO1 MUTATED LEO1 WILD-TYPE
  T1            0            184
  T2            3             91
  T3            2             77
  T4            0             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V5, binary
                cls
clus               0   1
  LEO1 MUTATED     5   0
  LEO1 WILD-TYPE 249   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  LEO1 MUTATED      5    0
  LEO1 WILD-TYPE  249    4
   clus
vv  LEO1 MUTATED LEO1 WILD-TYPE
  0            5            249
  1            0              4
[1] 2 2
[1] FALSE
D76V6, binary
                cls
clus               0   1
  LEO1 MUTATED     5   0
  LEO1 WILD-TYPE 264   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  LEO1 MUTATED      5    0
  LEO1 WILD-TYPE  264    4
   clus
vv  LEO1 MUTATED LEO1 WILD-TYPE
  0            5            264
  1            0              4
[1] 2 2
[1] FALSE
D76V7, binary
                cls
clus               0   1
  LEO1 MUTATED     0   5
  LEO1 WILD-TYPE 121 247
[1] "tbl2"
                cls
clus             [,1] [,2]
  LEO1 MUTATED      0    5
  LEO1 WILD-TYPE  121  247
        clus
vv       LEO1 MUTATED LEO1 WILD-TYPE
  FEMALE            0            121
  MALE              5            247
[1] 2 2
[1] FALSE
D76V8, binary
                cls
clus               0   1
  LEO1 MUTATED     4   1
  LEO1 WILD-TYPE 337   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  LEO1 MUTATED      4    1
  LEO1 WILD-TYPE  337    8
     clus
vv    LEO1 MUTATED LEO1 WILD-TYPE
  NO             4            337
  YES            1              8
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  LEO1 MUTATED                         0                        5
  LEO1 WILD-TYPE                       3                      358
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  LEO1 MUTATED                                  0
  LEO1 WILD-TYPE                                7
D76V9, multiclass
                                  clus
vv                                 LEO1 MUTATED LEO1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              3
  HEPATOCELLULAR CARCINOMA                    5            358
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  LEO1 MUTATED     4   0   0   1
  LEO1 WILD-TYPE 323  16   1  21
D76V10, multiclass
    clus
vv   LEO1 MUTATED LEO1 WILD-TYPE
  R0            4            323
  R1            0             16
  R2            0              1
  RX            1             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LEO1 MUTATED                                  0     4
  LEO1 WILD-TYPE                                2   156
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LEO1 MUTATED                           0     1
  LEO1 WILD-TYPE                        17   183
D76V11, multiclass
                                  clus
vv                                 LEO1 MUTATED LEO1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       4            156
  BLACK OR AFRICAN AMERICAN                   0             17
  WHITE                                       1            183
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V12, binary
                cls
clus               0   1
  LEO1 MUTATED     0   5
  LEO1 WILD-TYPE  18 332
[1] "tbl2"
                cls
clus             [,1] [,2]
  LEO1 MUTATED      0    5
  LEO1 WILD-TYPE   18  332
                        clus
vv                       LEO1 MUTATED LEO1 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            5            332
[1] 2 2
[1] FALSE

Clustering(77) Variable = CD97 MUTATION ANALYSIS
D77V1, survival
                sevent
clus2              0   1
  CD97 MUTATED     3   2
  CD97 WILD-TYPE 234 128
  CD97 MUTATED CD97 WILD-TYPE 
             5            362 
  CD97 MUTATED CD97 WILD-TYPE 
             2            128 
$`CD97 MUTATED`
TCGA-DD-A3A0 TCGA-DD-A73D TCGA-DD-AACL TCGA-DD-AAE0 TCGA-G3-A3CJ 
       25.81        22.78         3.52        18.25        19.53 

$`CD97 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       21.34         9.83        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
        9.14         9.86         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.15        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65        11.47        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       45.11        49.15         6.02        33.04        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 
       21.14        27.19        55.69         5.62        19.76         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       30.61        33.14        32.52        21.70        30.97        26.37 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
        9.30        23.05         1.45        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        75.65        76.41        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       71.80        12.00        15.42         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        0.30        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       34.49        20.91         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
       14.33        66.67        15.58        18.21        19.30        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 
       18.15        20.98        18.61        19.99         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       15.72        25.08        26.63        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       90.48        89.69        82.62        59.93        72.39        80.71 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       60.99        53.69        29.92        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         9.73         0.20        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       13.15        13.41        13.35         1.84         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       19.99        20.61        19.59         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI 
       14.86        21.53        25.64         5.92        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
       22.95        24.46        20.42        17.10        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       11.87        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  CD97 MUTATED CD97 WILD-TYPE 
          3.52           0.03 
  CD97 MUTATED CD97 WILD-TYPE 
         25.81         120.82 
  CD97 MUTATED CD97 WILD-TYPE 
        19.530         19.775 
[1] "3.5 - 25.8 (19.5)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.5"
D77V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CD97 MUTATED         2        2         0          1          0          0
  CD97 WILD-TYPE     172       84         3         63          9          9
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  CD97 MUTATED          0         0         0
  CD97 WILD-TYPE        2         1         2
D77V3, multiclass
            clus
vv           CD97 MUTATED CD97 WILD-TYPE
  STAGE I               2            172
  STAGE II              2             84
  STAGE III             0              3
  STAGE IIIA            1             63
  STAGE IIIB            0              9
  STAGE IIIC            0              9
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CD97 MUTATED     2   2   1   0
  CD97 WILD-TYPE 182  92  78  13
D77V4, multiclass
    clus
vv   CD97 MUTATED CD97 WILD-TYPE
  T1            2            182
  T2            2             92
  T3            1             78
  T4            0             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V5, binary
                cls
clus               0   1
  CD97 MUTATED     3   0
  CD97 WILD-TYPE 251   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD97 MUTATED      3    0
  CD97 WILD-TYPE  251    4
   clus
vv  CD97 MUTATED CD97 WILD-TYPE
  0            3            251
  1            0              4
[1] 2 2
[1] FALSE
D77V6, binary
                cls
clus               0   1
  CD97 MUTATED     4   0
  CD97 WILD-TYPE 265   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD97 MUTATED      4    0
  CD97 WILD-TYPE  265    4
   clus
vv  CD97 MUTATED CD97 WILD-TYPE
  0            4            265
  1            0              4
[1] 2 2
[1] FALSE
D77V7, binary
                cls
clus               0   1
  CD97 MUTATED     3   2
  CD97 WILD-TYPE 118 250
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD97 MUTATED      3    2
  CD97 WILD-TYPE  118  250
        clus
vv       CD97 MUTATED CD97 WILD-TYPE
  FEMALE            3            118
  MALE              2            250
[1] 2 2
[1] FALSE
D77V8, binary
                cls
clus               0   1
  CD97 MUTATED     5   0
  CD97 WILD-TYPE 336   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD97 MUTATED      5    0
  CD97 WILD-TYPE  336    9
     clus
vv    CD97 MUTATED CD97 WILD-TYPE
  NO             5            336
  YES            0              9
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  CD97 MUTATED                         0                        5
  CD97 WILD-TYPE                       3                      358
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  CD97 MUTATED                                  0
  CD97 WILD-TYPE                                7
D77V9, multiclass
                                  clus
vv                                 CD97 MUTATED CD97 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              3
  HEPATOCELLULAR CARCINOMA                    5            358
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CD97 MUTATED     5   0   0   0
  CD97 WILD-TYPE 322  16   1  22
D77V10, multiclass
    clus
vv   CD97 MUTATED CD97 WILD-TYPE
  R0            5            322
  R1            0             16
  R2            0              1
  RX            0             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD97 MUTATED                                  1     2
  CD97 WILD-TYPE                                1   158
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CD97 MUTATED                           0     2
  CD97 WILD-TYPE                        17   182
D77V11, multiclass
                                  clus
vv                                 CD97 MUTATED CD97 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              1
  ASIAN                                       2            158
  BLACK OR AFRICAN AMERICAN                   0             17
  WHITE                                       2            182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V12, binary
                cls
clus               0   1
  CD97 MUTATED     0   5
  CD97 WILD-TYPE  18 332
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD97 MUTATED      0    5
  CD97 WILD-TYPE   18  332
                        clus
vv                       CD97 MUTATED CD97 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            5            332
[1] 2 2
[1] FALSE

Clustering(78) Variable = SKA3 MUTATION ANALYSIS
D78V1, survival
                sevent
clus2              0   1
  SKA3 MUTATED     1   3
  SKA3 WILD-TYPE 236 127
  SKA3 MUTATED SKA3 WILD-TYPE 
             4            363 
  SKA3 MUTATED SKA3 WILD-TYPE 
             3            127 
$`SKA3 MUTATED`
TCGA-DD-A119 TCGA-DD-AAC8 TCGA-DD-AADY TCGA-G3-A25Y 
        7.33         0.53        18.25        14.86 

$`SKA3 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       21.34         9.83        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
        9.14         9.86         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.15        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65        11.47        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       27.19        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       30.61        33.14        32.52        21.70        30.97        26.37 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
       13.48        11.41        75.65        76.41        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       71.80        12.00        15.42         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
        0.30         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       14.20        59.31        51.35        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.05        34.49        20.91         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        89.69        82.62        59.93        72.39 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        60.99        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        20.61        19.59         0.62        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 
       14.40        60.89        23.97        19.10        27.88        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.03         0.33         0.39        13.68        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       28.27        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       25.25        22.95        24.46        20.42        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       20.78        11.87        14.14        15.78        15.65        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       12.23        13.55         0.89        11.64         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       58.88        26.27        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        22.78        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        25.71        23.21        35.87        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  SKA3 MUTATED SKA3 WILD-TYPE 
          0.53           0.03 
  SKA3 MUTATED SKA3 WILD-TYPE 
         18.25         120.82 
  SKA3 MUTATED SKA3 WILD-TYPE 
        11.095         19.990 
[1] "0.5 - 18.2 (11.1)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "5"  
D78V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  SKA3 MUTATED         3        0         0          0          0          0
  SKA3 WILD-TYPE     171       86         3         64          9          9
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  SKA3 MUTATED          1         0         0
  SKA3 WILD-TYPE        1         1         2
D78V3, multiclass
            clus
vv           SKA3 MUTATED SKA3 WILD-TYPE
  STAGE I               3            171
  STAGE II              0             86
  STAGE III             0              3
  STAGE IIIA            0             64
  STAGE IIIB            0              9
  STAGE IIIC            0              9
  STAGE IV              1              1
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SKA3 MUTATED     3   0   1   0
  SKA3 WILD-TYPE 181  94  78  13
D78V4, multiclass
    clus
vv   SKA3 MUTATED SKA3 WILD-TYPE
  T1            3            181
  T2            0             94
  T3            1             78
  T4            0             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V5, binary
                cls
clus               0   1
  SKA3 MUTATED     4   0
  SKA3 WILD-TYPE 250   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  SKA3 MUTATED      4    0
  SKA3 WILD-TYPE  250    4
   clus
vv  SKA3 MUTATED SKA3 WILD-TYPE
  0            4            250
  1            0              4
[1] 2 2
[1] FALSE
D78V6, binary
                cls
clus               0   1
  SKA3 MUTATED     3   1
  SKA3 WILD-TYPE 266   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  SKA3 MUTATED      3    1
  SKA3 WILD-TYPE  266    3
   clus
vv  SKA3 MUTATED SKA3 WILD-TYPE
  0            3            266
  1            1              3
[1] 2 2
[1] FALSE
D78V7, binary
                cls
clus               0   1
  SKA3 MUTATED     2   2
  SKA3 WILD-TYPE 119 250
[1] "tbl2"
                cls
clus             [,1] [,2]
  SKA3 MUTATED      2    2
  SKA3 WILD-TYPE  119  250
        clus
vv       SKA3 MUTATED SKA3 WILD-TYPE
  FEMALE            2            119
  MALE              2            250
[1] 2 2
[1] FALSE
D78V8, binary
                cls
clus               0   1
  SKA3 MUTATED     3   0
  SKA3 WILD-TYPE 338   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  SKA3 MUTATED      3    0
  SKA3 WILD-TYPE  338    9
     clus
vv    SKA3 MUTATED SKA3 WILD-TYPE
  NO             3            338
  YES            0              9
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  SKA3 MUTATED                         0                        4
  SKA3 WILD-TYPE                       3                      359
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  SKA3 MUTATED                                  0
  SKA3 WILD-TYPE                                7
D78V9, multiclass
                                  clus
vv                                 SKA3 MUTATED SKA3 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              3
  HEPATOCELLULAR CARCINOMA                    4            359
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SKA3 MUTATED     3   0   1   0
  SKA3 WILD-TYPE 324  16   0  22
D78V10, multiclass
    clus
vv   SKA3 MUTATED SKA3 WILD-TYPE
  R0            3            324
  R1            0             16
  R2            1              0
  RX            0             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SKA3 MUTATED                                  0     4
  SKA3 WILD-TYPE                                2   156
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SKA3 MUTATED                           0     0
  SKA3 WILD-TYPE                        17   184
D78V11, multiclass
                                  clus
vv                                 SKA3 MUTATED SKA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       4            156
  BLACK OR AFRICAN AMERICAN                   0             17
  WHITE                                       0            184
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V12, binary
                cls
clus               0   1
  SKA3 MUTATED     0   4
  SKA3 WILD-TYPE  18 333
[1] "tbl2"
                cls
clus             [,1] [,2]
  SKA3 MUTATED      0    4
  SKA3 WILD-TYPE   18  333
                        clus
vv                       SKA3 MUTATED SKA3 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            4            333
[1] 2 2
[1] FALSE

Clustering(79) Variable = CBX4 MUTATION ANALYSIS
D79V1, survival
                sevent
clus2              0   1
  CBX4 MUTATED     2   4
  CBX4 WILD-TYPE 235 126
  CBX4 MUTATED CBX4 WILD-TYPE 
             6            361 
  CBX4 MUTATED CBX4 WILD-TYPE 
             4            126 
$`CBX4 MUTATED`
TCGA-BC-A112 TCGA-G3-A7M9 TCGA-5C-A9VH TCGA-DD-A39Y TCGA-DD-AACG TCGA-G3-A7M6 
        5.03         1.84        10.59         5.62        15.42        20.78 

$`CBX4 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-K7-A5RF 
        6.38        81.73        30.74        22.13        22.06        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
        2.14        31.27        12.72        24.56         0.76         7.04 
TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
       10.32        44.02        29.52         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
      120.82        40.41        56.91        49.84        47.74        18.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       20.81        22.92         1.18         8.55        13.02        10.78 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q 
        0.66        17.10        14.76         1.51        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       10.13        27.52        27.52         2.99        25.32        23.38 
TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        1.12        44.42        45.93         0.26        22.36        14.60 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 
       18.48        44.81        13.45         0.66         4.24         8.22 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 
        2.86         3.19         3.39         4.24         3.35         7.20 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.32         9.86         9.96        10.36        11.93        11.41 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
        9.99         8.94         7.13        21.34         9.83        12.00 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT 
       13.12        12.56         8.61         9.14         9.86         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 
       11.31         9.17         6.94         8.15        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65        11.47        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       21.70        30.97        26.37        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        71.80        12.00 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       42.81        61.68        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
        0.39        29.52        14.89        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       25.08        26.63        25.78        50.33        35.08        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       89.69        82.62        59.93        72.39        80.71        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        60.99 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        9.73         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.39        13.68        51.06        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M7 
       22.95        24.46        20.42        17.10        14.70        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        0.89        11.64         2.14        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       27.25        29.79        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       22.95        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       17.69        21.01         3.09         0.72         0.49         0.30 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.04        19.33        19.04        15.39        15.52        36.10 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       27.88        19.76        16.44         1.71        15.98        10.75 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       11.34         0.99        12.99        20.22        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        22.78        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.21        35.87        25.15        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  CBX4 MUTATED CBX4 WILD-TYPE 
          1.84           0.03 
  CBX4 MUTATED CBX4 WILD-TYPE 
         20.78         120.82 
  CBX4 MUTATED CBX4 WILD-TYPE 
         8.105         19.990 
[1] "1.8 - 20.8 (8.1)"   "0.0 - 120.8 (20.0)"
[1] "hr=" "4.5"
D79V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CBX4 MUTATED         3        1         0          0          1          0
  CBX4 WILD-TYPE     171       85         3         64          8          9
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  CBX4 MUTATED          0         0         0
  CBX4 WILD-TYPE        2         1         2
D79V3, multiclass
            clus
vv           CBX4 MUTATED CBX4 WILD-TYPE
  STAGE I               3            171
  STAGE II              1             85
  STAGE III             0              3
  STAGE IIIA            0             64
  STAGE IIIB            1              8
  STAGE IIIC            0              9
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CBX4 MUTATED     3   1   2   0
  CBX4 WILD-TYPE 181  93  77  13
D79V4, multiclass
    clus
vv   CBX4 MUTATED CBX4 WILD-TYPE
  T1            3            181
  T2            1             93
  T3            2             77
  T4            0             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V5, binary
                cls
clus               0   1
  CBX4 MUTATED     2   0
  CBX4 WILD-TYPE 252   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX4 MUTATED      2    0
  CBX4 WILD-TYPE  252    4
   clus
vv  CBX4 MUTATED CBX4 WILD-TYPE
  0            2            252
  1            0              4
[1] 2 2
[1] FALSE
D79V6, binary
                cls
clus               0   1
  CBX4 MUTATED     3   0
  CBX4 WILD-TYPE 266   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX4 MUTATED      3    0
  CBX4 WILD-TYPE  266    4
   clus
vv  CBX4 MUTATED CBX4 WILD-TYPE
  0            3            266
  1            0              4
[1] 2 2
[1] FALSE
D79V7, binary
                cls
clus               0   1
  CBX4 MUTATED     1   5
  CBX4 WILD-TYPE 120 247
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX4 MUTATED      1    5
  CBX4 WILD-TYPE  120  247
        clus
vv       CBX4 MUTATED CBX4 WILD-TYPE
  FEMALE            1            120
  MALE              5            247
[1] 2 2
[1] FALSE
D79V8, binary
                cls
clus               0   1
  CBX4 MUTATED     6   0
  CBX4 WILD-TYPE 335   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX4 MUTATED      6    0
  CBX4 WILD-TYPE  335    9
     clus
vv    CBX4 MUTATED CBX4 WILD-TYPE
  NO             6            335
  YES            0              9
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  CBX4 MUTATED                         0                        6
  CBX4 WILD-TYPE                       3                      357
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  CBX4 MUTATED                                  0
  CBX4 WILD-TYPE                                7
D79V9, multiclass
                                  clus
vv                                 CBX4 MUTATED CBX4 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              3
  HEPATOCELLULAR CARCINOMA                    6            357
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CBX4 MUTATED     6   0   0   0
  CBX4 WILD-TYPE 321  16   1  22
D79V10, multiclass
    clus
vv   CBX4 MUTATED CBX4 WILD-TYPE
  R0            6            321
  R1            0             16
  R2            0              1
  RX            0             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CBX4 MUTATED                                  0     2
  CBX4 WILD-TYPE                                2   158
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CBX4 MUTATED                           0     4
  CBX4 WILD-TYPE                        17   180
D79V11, multiclass
                                  clus
vv                                 CBX4 MUTATED CBX4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       2            158
  BLACK OR AFRICAN AMERICAN                   0             17
  WHITE                                       4            180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V12, binary
                cls
clus               0   1
  CBX4 MUTATED     0   6
  CBX4 WILD-TYPE  18 331
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX4 MUTATED      0    6
  CBX4 WILD-TYPE   18  331
                        clus
vv                       CBX4 MUTATED CBX4 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            6            331
[1] 2 2
[1] FALSE

Clustering(80) Variable = MTA1 MUTATION ANALYSIS
D80V1, survival
                sevent
clus2              0   1
  MTA1 MUTATED     1   4
  MTA1 WILD-TYPE 236 126
  MTA1 MUTATED MTA1 WILD-TYPE 
             5            362 
  MTA1 MUTATED MTA1 WILD-TYPE 
             4            126 
$`MTA1 MUTATED`
TCGA-DD-A1EG TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-AACQ TCGA-MI-A75I 
       45.11         5.62         7.66        14.20        20.71 

$`MTA1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       21.34         9.83        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
        9.14         9.86         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.15        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF 
       79.40        66.31        19.79        75.65        11.47        12.95 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 
       27.19        55.69        19.76        25.81        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ 
       32.52        21.70        30.97        26.37        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACS 
        3.52        58.16        42.81        61.68        13.64        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        40.08        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        29.52        14.89        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       66.67        15.58        18.21        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 
       18.15        20.98        18.61        19.99         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       15.72        25.08        26.63        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       90.48        89.69        82.62        59.93        72.39        80.71 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       60.99        53.69        29.92        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         9.73         0.20        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       13.15        13.41        13.35         1.84         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       19.99        20.61        19.59         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       25.25        22.95        24.46        20.42        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       20.78        11.87        14.14        15.78        15.65        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       12.23        13.55         0.89        11.64         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
        9.57        16.67        22.95         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  MTA1 MUTATED MTA1 WILD-TYPE 
          5.62           0.03 
  MTA1 MUTATED MTA1 WILD-TYPE 
         45.11         120.82 
  MTA1 MUTATED MTA1 WILD-TYPE 
        14.200         19.775 
[1] "5.6 - 45.1 (14.2)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "3.2"
D80V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  MTA1 MUTATED         2        1         0          2          0          0
  MTA1 WILD-TYPE     172       85         3         62          9          9
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  MTA1 MUTATED          0         0         0
  MTA1 WILD-TYPE        2         1         2
D80V3, multiclass
            clus
vv           MTA1 MUTATED MTA1 WILD-TYPE
  STAGE I               2            172
  STAGE II              1             85
  STAGE III             0              3
  STAGE IIIA            2             62
  STAGE IIIB            0              9
  STAGE IIIC            0              9
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MTA1 MUTATED     2   2   2   0
  MTA1 WILD-TYPE 182  92  77  13
D80V4, multiclass
    clus
vv   MTA1 MUTATED MTA1 WILD-TYPE
  T1            2            182
  T2            2             92
  T3            2             77
  T4            0             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V5, binary
                cls
clus               0   1
  MTA1 MUTATED     4   0
  MTA1 WILD-TYPE 250   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTA1 MUTATED      4    0
  MTA1 WILD-TYPE  250    4
   clus
vv  MTA1 MUTATED MTA1 WILD-TYPE
  0            4            250
  1            0              4
[1] 2 2
[1] FALSE
D80V6, binary
                cls
clus               0   1
  MTA1 MUTATED     5   0
  MTA1 WILD-TYPE 264   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTA1 MUTATED      5    0
  MTA1 WILD-TYPE  264    4
   clus
vv  MTA1 MUTATED MTA1 WILD-TYPE
  0            5            264
  1            0              4
[1] 2 2
[1] FALSE
D80V7, binary
                cls
clus               0   1
  MTA1 MUTATED     0   6
  MTA1 WILD-TYPE 121 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTA1 MUTATED      0    6
  MTA1 WILD-TYPE  121  246
        clus
vv       MTA1 MUTATED MTA1 WILD-TYPE
  FEMALE            0            121
  MALE              6            246
[1] 2 2
[1] FALSE
D80V8, binary
                cls
clus               0   1
  MTA1 MUTATED     5   0
  MTA1 WILD-TYPE 336   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTA1 MUTATED      5    0
  MTA1 WILD-TYPE  336    9
     clus
vv    MTA1 MUTATED MTA1 WILD-TYPE
  NO             5            336
  YES            0              9
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  MTA1 MUTATED                         0                        6
  MTA1 WILD-TYPE                       3                      357
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  MTA1 MUTATED                                  0
  MTA1 WILD-TYPE                                7
D80V9, multiclass
                                  clus
vv                                 MTA1 MUTATED MTA1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              3
  HEPATOCELLULAR CARCINOMA                    6            357
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MTA1 MUTATED     6   0   0   0
  MTA1 WILD-TYPE 321  16   1  22
D80V10, multiclass
    clus
vv   MTA1 MUTATED MTA1 WILD-TYPE
  R0            6            321
  R1            0             16
  R2            0              1
  RX            0             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MTA1 MUTATED                                  0     3
  MTA1 WILD-TYPE                                2   157
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MTA1 MUTATED                           1     1
  MTA1 WILD-TYPE                        16   183
D80V11, multiclass
                                  clus
vv                                 MTA1 MUTATED MTA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       3            157
  BLACK OR AFRICAN AMERICAN                   1             16
  WHITE                                       1            183
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V12, binary
                cls
clus               0   1
  MTA1 MUTATED     0   5
  MTA1 WILD-TYPE  18 332
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTA1 MUTATED      0    5
  MTA1 WILD-TYPE   18  332
                        clus
vv                       MTA1 MUTATED MTA1 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            5            332
[1] 2 2
[1] FALSE

Clustering(81) Variable = CRIP3 MUTATION ANALYSIS
D81V1, survival
                 sevent
clus2               0   1
  CRIP3 MUTATED     3   3
  CRIP3 WILD-TYPE 234 127
  CRIP3 MUTATED CRIP3 WILD-TYPE 
              6             361 
  CRIP3 MUTATED CRIP3 WILD-TYPE 
              3             127 
$`CRIP3 MUTATED`
TCGA-KR-A7K7 TCGA-DD-A1EE TCGA-DD-AADM TCGA-DD-AAEH TCGA-DD-AAVP TCGA-G3-A25S 
       31.27        11.47         0.39        25.78        90.48        13.68 

$`CRIP3 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
        1.84        20.75         2.14        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        20.81        22.92         1.18         8.55        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        17.10        14.76         1.51 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        14.60        18.48        44.81        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.24         8.22         2.86         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.35         7.20         3.32         9.86         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
       11.93        11.41         9.99         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        9.83        12.00        13.12        12.56         8.61         9.14 
TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.86         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       66.31        19.79        75.65        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       33.14        32.52        21.70        30.97        26.37        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       23.05        22.78         1.45        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        75.65        76.41        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       71.80        12.00        15.42         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
        0.30         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       14.20        59.31        51.35        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       35.05        34.49        20.91        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
       14.33        66.67        15.58        18.21        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEI TCGA-DD-AAEK 
       23.74        15.72        25.08        26.63        50.33        35.08 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       89.69        82.62        59.93        72.39        80.71        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        60.99 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        9.73         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z 
        0.39        51.06        53.79        28.27        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        25.25        22.95 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       24.46        20.42        17.10        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        0.89        11.64         2.14        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       27.25        29.79        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       22.95        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       17.69        21.01         3.09         0.72         0.49         0.30 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.04        19.33        19.04        15.39        15.52        36.10 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       27.88        19.76        16.44         1.71        15.98        10.75 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       11.34         0.99        12.99        20.22        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        22.78        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.21        35.87        25.15        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  CRIP3 MUTATED CRIP3 WILD-TYPE 
           0.39            0.03 
  CRIP3 MUTATED CRIP3 WILD-TYPE 
          90.48          120.82 
  CRIP3 MUTATED CRIP3 WILD-TYPE 
          19.73           19.76 
[1] "0.4 - 90.5 (19.7)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.3"
D81V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CRIP3 MUTATED         3        2         0          1          0          0
  CRIP3 WILD-TYPE     171       84         3         63          9          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  CRIP3 MUTATED          0         0         0
  CRIP3 WILD-TYPE        2         1         2
D81V3, multiclass
            clus
vv           CRIP3 MUTATED CRIP3 WILD-TYPE
  STAGE I                3             171
  STAGE II               2              84
  STAGE III              0               3
  STAGE IIIA             1              63
  STAGE IIIB             0               9
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CRIP3 MUTATED     3   2   1   0
  CRIP3 WILD-TYPE 181  92  78  13
D81V4, multiclass
    clus
vv   CRIP3 MUTATED CRIP3 WILD-TYPE
  T1             3             181
  T2             2              92
  T3             1              78
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V5, binary
                 cls
clus                0   1
  CRIP3 MUTATED     6   0
  CRIP3 WILD-TYPE 248   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRIP3 MUTATED      6    0
  CRIP3 WILD-TYPE  248    4
   clus
vv  CRIP3 MUTATED CRIP3 WILD-TYPE
  0             6             248
  1             0               4
[1] 2 2
[1] FALSE
D81V6, binary
                 cls
clus                0   1
  CRIP3 MUTATED     6   0
  CRIP3 WILD-TYPE 263   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRIP3 MUTATED      6    0
  CRIP3 WILD-TYPE  263    4
   clus
vv  CRIP3 MUTATED CRIP3 WILD-TYPE
  0             6             263
  1             0               4
[1] 2 2
[1] FALSE
D81V7, binary
                 cls
clus                0   1
  CRIP3 MUTATED     1   5
  CRIP3 WILD-TYPE 120 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRIP3 MUTATED      1    5
  CRIP3 WILD-TYPE  120  247
        clus
vv       CRIP3 MUTATED CRIP3 WILD-TYPE
  FEMALE             1             120
  MALE               5             247
[1] 2 2
[1] FALSE
D81V8, binary
                 cls
clus                0   1
  CRIP3 MUTATED     6   0
  CRIP3 WILD-TYPE 335   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRIP3 MUTATED      6    0
  CRIP3 WILD-TYPE  335    9
     clus
vv    CRIP3 MUTATED CRIP3 WILD-TYPE
  NO              6             335
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  CRIP3 MUTATED                         0                        6
  CRIP3 WILD-TYPE                       3                      357
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  CRIP3 MUTATED                                  0
  CRIP3 WILD-TYPE                                7
D81V9, multiclass
                                  clus
vv                                 CRIP3 MUTATED CRIP3 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                     6             357
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CRIP3 MUTATED     5   1   0   0
  CRIP3 WILD-TYPE 322  15   1  22
D81V10, multiclass
    clus
vv   CRIP3 MUTATED CRIP3 WILD-TYPE
  R0             5             322
  R1             1              15
  R2             0               1
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CRIP3 MUTATED                                  0     3
  CRIP3 WILD-TYPE                                2   157
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CRIP3 MUTATED                           0     3
  CRIP3 WILD-TYPE                        17   181
D81V11, multiclass
                                  clus
vv                                 CRIP3 MUTATED CRIP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        3             157
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        3             181
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V12, binary
                 cls
clus                0   1
  CRIP3 MUTATED     0   5
  CRIP3 WILD-TYPE  18 332
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRIP3 MUTATED      0    5
  CRIP3 WILD-TYPE   18  332
                        clus
vv                       CRIP3 MUTATED CRIP3 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             5             332
[1] 2 2
[1] FALSE

Clustering(82) Variable = NR4A2 MUTATION ANALYSIS
D82V1, survival
                 sevent
clus2               0   1
  NR4A2 MUTATED     1   5
  NR4A2 WILD-TYPE 236 125
  NR4A2 MUTATED NR4A2 WILD-TYPE 
              6             361 
  NR4A2 MUTATED NR4A2 WILD-TYPE 
              5             125 
$`NR4A2 MUTATED`
TCGA-UB-A7MF TCGA-CC-5263 TCGA-DD-A1EE TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-RC-A6M4 
        7.04         4.24        11.47         5.62        25.81         0.72 

$`NR4A2 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        0.76        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        20.81        22.92         1.18         8.55        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        17.10        14.76         1.51 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        14.60        18.48        44.81        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5264 
        4.24         8.22         2.86         3.19         3.39         3.35 
TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        7.20         3.32         9.86         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS 
       12.00        13.12        12.56         8.61         9.14         9.86 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.76         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE 
      107.11        13.78        30.61        33.14        32.52        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        26.37        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA 
       35.67       114.35        13.48         0.53        11.41        75.65 
TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG 
       76.41        55.40        12.53        71.80        12.00        15.42 
TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM 
        6.41        53.19        69.11         0.30         3.52        58.16 
TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT 
       42.81        61.68        13.64        14.20        59.31        51.35 
TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ 
       51.52        50.33        46.82         5.59        47.67         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
        0.39        29.52        14.89        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       25.08        26.63        25.78        50.33        35.08        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       89.69        82.62        59.93        72.39        80.71        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        60.99 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        9.73         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.39        13.68        51.06        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
       22.95        24.46        20.42        17.10        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       11.87        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M5 TCGA-RC-A6M6 
       26.27        17.69        21.01         3.09         0.49         0.30 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.04        19.33        19.04        15.39        15.52        36.10 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       27.88        19.76        16.44         1.71        15.98        10.75 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       11.34         0.99        12.99        20.22        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        22.78        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.21        35.87        25.15        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  NR4A2 MUTATED NR4A2 WILD-TYPE 
           0.72            0.03 
  NR4A2 MUTATED NR4A2 WILD-TYPE 
          25.81          120.82 
  NR4A2 MUTATED NR4A2 WILD-TYPE 
           6.33           19.99 
[1] "0.7 - 25.8 (6.3)"   "0.0 - 120.8 (20.0)"
[1] "hr=" "6.1"
D82V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  NR4A2 MUTATED         2        0         0          4          0          0
  NR4A2 WILD-TYPE     172       86         3         60          9          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  NR4A2 MUTATED          0         0         0
  NR4A2 WILD-TYPE        2         1         2
D82V3, multiclass
            clus
vv           NR4A2 MUTATED NR4A2 WILD-TYPE
  STAGE I                2             172
  STAGE II               0              86
  STAGE III              0               3
  STAGE IIIA             4              60
  STAGE IIIB             0               9
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NR4A2 MUTATED     2   0   4   0
  NR4A2 WILD-TYPE 182  94  75  13
D82V4, multiclass
    clus
vv   NR4A2 MUTATED NR4A2 WILD-TYPE
  T1             2             182
  T2             0              94
  T3             4              75
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V5, binary
                 cls
clus                0   1
  NR4A2 MUTATED     2   0
  NR4A2 WILD-TYPE 252   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR4A2 MUTATED      2    0
  NR4A2 WILD-TYPE  252    4
   clus
vv  NR4A2 MUTATED NR4A2 WILD-TYPE
  0             2             252
  1             0               4
[1] 2 2
[1] FALSE
D82V6, binary
                 cls
clus                0   1
  NR4A2 MUTATED     4   0
  NR4A2 WILD-TYPE 265   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR4A2 MUTATED      4    0
  NR4A2 WILD-TYPE  265    4
   clus
vv  NR4A2 MUTATED NR4A2 WILD-TYPE
  0             4             265
  1             0               4
[1] 2 2
[1] FALSE
D82V7, binary
                 cls
clus                0   1
  NR4A2 MUTATED     1   5
  NR4A2 WILD-TYPE 120 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR4A2 MUTATED      1    5
  NR4A2 WILD-TYPE  120  247
        clus
vv       NR4A2 MUTATED NR4A2 WILD-TYPE
  FEMALE             1             120
  MALE               5             247
[1] 2 2
[1] FALSE
D82V8, binary
                 cls
clus                0   1
  NR4A2 MUTATED     5   0
  NR4A2 WILD-TYPE 336   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR4A2 MUTATED      5    0
  NR4A2 WILD-TYPE  336    9
     clus
vv    NR4A2 MUTATED NR4A2 WILD-TYPE
  NO              5             336
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  NR4A2 MUTATED                         0                        6
  NR4A2 WILD-TYPE                       3                      357
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  NR4A2 MUTATED                                  0
  NR4A2 WILD-TYPE                                7
D82V9, multiclass
                                  clus
vv                                 NR4A2 MUTATED NR4A2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                     6             357
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NR4A2 MUTATED     4   1   0   1
  NR4A2 WILD-TYPE 323  15   1  21
D82V10, multiclass
    clus
vv   NR4A2 MUTATED NR4A2 WILD-TYPE
  R0             4             323
  R1             1              15
  R2             0               1
  RX             1              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NR4A2 MUTATED                                  0     2
  NR4A2 WILD-TYPE                                2   158
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NR4A2 MUTATED                           0     4
  NR4A2 WILD-TYPE                        17   180
D82V11, multiclass
                                  clus
vv                                 NR4A2 MUTATED NR4A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        2             158
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        4             180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V12, binary
                 cls
clus                0   1
  NR4A2 MUTATED     0   6
  NR4A2 WILD-TYPE  18 331
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR4A2 MUTATED      0    6
  NR4A2 WILD-TYPE   18  331
                        clus
vv                       NR4A2 MUTATED NR4A2 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             6             331
[1] 2 2
[1] FALSE

Clustering(83) Variable = HNF1A MUTATION ANALYSIS
D83V1, survival
                 sevent
clus2               0   1
  HNF1A MUTATED     4   4
  HNF1A WILD-TYPE 233 126
  HNF1A MUTATED HNF1A WILD-TYPE 
              8             359 
  HNF1A MUTATED HNF1A WILD-TYPE 
              4             126 
$`HNF1A MUTATED`
TCGA-T1-A6J8 TCGA-CC-A3M9 TCGA-DD-A1EB TCGA-DD-A39W TCGA-DD-A3A2 TCGA-DD-A73C 
        0.76         9.86        66.31        27.19        70.06        23.05 
TCGA-NI-A4U2 TCGA-WJ-A86L 
       58.88        11.34 

$`HNF1A WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        20.81        22.92         1.18         8.55        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        17.10        14.76         1.51 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        14.60        18.48        44.81        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.24         8.22         2.86         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        3.35         7.20         3.32         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS 
       12.00        13.12        12.56         8.61         9.14         9.86 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC 
        0.46        21.76        51.29        90.71        79.40        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65        11.47        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       33.04        18.35        13.64        21.14        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.76        25.81         7.66        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE 
      107.11        13.78        30.61        33.14        32.52        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        26.37        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       78.84        23.93         9.30        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
      114.35        13.48         0.53        11.41        75.65        76.41 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
       55.40        12.53        71.80        12.00        15.42         6.41 
TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN 
       53.19        69.11         0.30         3.52        58.16        42.81 
TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
       61.68        13.64        14.20        59.31        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       50.33        46.82         5.59        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       40.54        40.83        13.97        40.47        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM 
       37.64        35.67        35.05        34.49        20.91         0.39 
TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS 
       29.52        14.89        15.06        14.33        66.67        15.58 
TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 
       18.21        19.30        18.25        18.25        18.15        20.98 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED 
       18.61        19.99         4.64        23.74        15.72        25.08 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ 
       26.63        25.78        50.33        35.08        90.48        89.69 
TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX 
       82.62        59.93        72.39        80.71        76.18        56.48 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 
       64.77        62.47        66.25        65.39        60.99        53.69 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       29.92        26.93        28.08        13.91        13.35         9.73 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20        12.82         0.20        14.04        13.15        13.41 
TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       13.35         1.84         0.20        18.74        19.99        20.61 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
       19.59         0.62        11.93        14.40        60.89        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
       19.10        27.88        12.03         0.03         0.33         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z 
       13.68        51.06        53.79        28.27        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        25.25        22.95 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       24.46        20.42        17.10        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        0.89        11.64         2.14        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       27.25        29.79        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A8LF TCGA-O8-A75V 
       22.95        20.71         7.53        10.85        26.27        17.69 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 
       21.01         3.09         0.72         0.49         0.30        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       19.33        19.04        15.39        15.52        36.10        27.88 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WQ-A9G7 
       19.76        16.44         1.71        15.98        10.75         0.99 
TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE 
       12.99        20.22        24.85        18.28        33.86        30.41 
TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       22.78        13.55        35.77        25.71        23.21        35.87 
TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.15        12.99        45.57        79.30        11.21 

  HNF1A MUTATED HNF1A WILD-TYPE 
           0.76            0.03 
  HNF1A MUTATED HNF1A WILD-TYPE 
          70.06          120.82 
  HNF1A MUTATED HNF1A WILD-TYPE 
          25.12           19.76 
[1] "0.8 - 70.1 (25.1)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.2"
D83V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  HNF1A MUTATED         3        0         1          3          0          0
  HNF1A WILD-TYPE     171       86         2         61          9          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  HNF1A MUTATED          0         0         0
  HNF1A WILD-TYPE        2         1         2
D83V3, multiclass
            clus
vv           HNF1A MUTATED HNF1A WILD-TYPE
  STAGE I                3             171
  STAGE II               0              86
  STAGE III              1               2
  STAGE IIIA             3              61
  STAGE IIIB             0               9
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HNF1A MUTATED     4   0   4   0
  HNF1A WILD-TYPE 180  94  75  13
D83V4, multiclass
    clus
vv   HNF1A MUTATED HNF1A WILD-TYPE
  T1             4             180
  T2             0              94
  T3             4              75
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V5, binary
                 cls
clus                0   1
  HNF1A MUTATED     5   0
  HNF1A WILD-TYPE 249   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1A MUTATED      5    0
  HNF1A WILD-TYPE  249    4
   clus
vv  HNF1A MUTATED HNF1A WILD-TYPE
  0             5             249
  1             0               4
[1] 2 2
[1] FALSE
D83V6, binary
                 cls
clus                0   1
  HNF1A MUTATED     6   0
  HNF1A WILD-TYPE 263   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1A MUTATED      6    0
  HNF1A WILD-TYPE  263    4
   clus
vv  HNF1A MUTATED HNF1A WILD-TYPE
  0             6             263
  1             0               4
[1] 2 2
[1] FALSE
D83V7, binary
                 cls
clus                0   1
  HNF1A MUTATED     5   3
  HNF1A WILD-TYPE 116 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1A MUTATED      5    3
  HNF1A WILD-TYPE  116  249
        clus
vv       HNF1A MUTATED HNF1A WILD-TYPE
  FEMALE             5             116
  MALE               3             249
[1] 2 2
[1] FALSE
D83V8, binary
                 cls
clus                0   1
  HNF1A MUTATED     6   0
  HNF1A WILD-TYPE 335   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1A MUTATED      6    0
  HNF1A WILD-TYPE  335    9
     clus
vv    HNF1A MUTATED HNF1A WILD-TYPE
  NO              6             335
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  HNF1A MUTATED                         0                        8
  HNF1A WILD-TYPE                       3                      355
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  HNF1A MUTATED                                  0
  HNF1A WILD-TYPE                                7
D83V9, multiclass
                                  clus
vv                                 HNF1A MUTATED HNF1A WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                     8             355
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HNF1A MUTATED     7   0   0   1
  HNF1A WILD-TYPE 320  16   1  21
D83V10, multiclass
    clus
vv   HNF1A MUTATED HNF1A WILD-TYPE
  R0             7             320
  R1             0              16
  R2             0               1
  RX             1              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HNF1A MUTATED                                  0     1
  HNF1A WILD-TYPE                                2   159
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HNF1A MUTATED                           0     6
  HNF1A WILD-TYPE                        17   178
D83V11, multiclass
                                  clus
vv                                 HNF1A MUTATED HNF1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1             159
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        6             178
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V12, binary
                 cls
clus                0   1
  HNF1A MUTATED     0   7
  HNF1A WILD-TYPE  18 330
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1A MUTATED      0    7
  HNF1A WILD-TYPE   18  330
                        clus
vv                       HNF1A MUTATED HNF1A WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             7             330
[1] 2 2
[1] FALSE

Clustering(84) Variable = KRAS MUTATION ANALYSIS
D84V1, survival
                sevent
clus2              0   1
  KRAS MUTATED     4   2
  KRAS WILD-TYPE 233 128
  KRAS MUTATED KRAS WILD-TYPE 
             6            361 
  KRAS MUTATED KRAS WILD-TYPE 
             2            128 
$`KRAS MUTATED`
TCGA-2Y-A9H7 TCGA-DD-A39Y TCGA-DD-A3A4 TCGA-DD-A4NB TCGA-DD-AADA TCGA-MI-A75C 
       38.40         5.62        20.12        32.52        40.54         9.57 

$`KRAS WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        11.74         8.61        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        20.81        22.92         1.18         8.55        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        17.10        14.76         1.51 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        14.60        18.48        44.81        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.24         8.22         2.86         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.35         7.20         3.32         9.86         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
       11.93        11.41         9.99         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        9.83        12.00        13.12        12.56         8.61         9.14 
TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.86         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65        11.47        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       27.19        55.69        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       17.59       102.74       107.11        13.78        30.61        33.14 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       21.70        30.97        26.37        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       22.09        40.08        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR 
        0.39        29.52        14.89        15.06        14.33        66.67 
TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       15.58        18.21        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       25.08        26.63        25.78        50.33        35.08        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       89.69        82.62        59.93        72.39        80.71        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        60.99 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        9.73         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.39        13.68        51.06        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
       22.95        24.46        20.42        17.10        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       11.87        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75E 
       11.80        27.25        29.79        13.97        12.03        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       22.95        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       17.69        21.01         3.09         0.72         0.49         0.30 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.04        19.33        19.04        15.39        15.52        36.10 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       27.88        19.76        16.44         1.71        15.98        10.75 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       11.34         0.99        12.99        20.22        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        22.78        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.21        35.87        25.15        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  KRAS MUTATED KRAS WILD-TYPE 
          5.62           0.03 
  KRAS MUTATED KRAS WILD-TYPE 
         40.54         120.82 
  KRAS MUTATED KRAS WILD-TYPE 
         26.32          19.76 
[1] "5.6 - 40.5 (26.3)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1"  
D84V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  KRAS MUTATED         5        0         0          1          0          0
  KRAS WILD-TYPE     169       86         3         63          9          9
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  KRAS MUTATED          0         0         0
  KRAS WILD-TYPE        2         1         2
D84V3, multiclass
            clus
vv           KRAS MUTATED KRAS WILD-TYPE
  STAGE I               5            169
  STAGE II              0             86
  STAGE III             0              3
  STAGE IIIA            1             63
  STAGE IIIB            0              9
  STAGE IIIC            0              9
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KRAS MUTATED     5   0   1   0
  KRAS WILD-TYPE 179  94  78  13
D84V4, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  T1            5            179
  T2            0             94
  T3            1             78
  T4            0             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V5, binary
                cls
clus               0   1
  KRAS MUTATED     5   0
  KRAS WILD-TYPE 249   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      5    0
  KRAS WILD-TYPE  249    4
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0            5            249
  1            0              4
[1] 2 2
[1] FALSE
D84V6, binary
                cls
clus               0   1
  KRAS MUTATED     5   0
  KRAS WILD-TYPE 264   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      5    0
  KRAS WILD-TYPE  264    4
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0            5            264
  1            0              4
[1] 2 2
[1] FALSE
D84V7, binary
                cls
clus               0   1
  KRAS MUTATED     2   4
  KRAS WILD-TYPE 119 248
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      2    4
  KRAS WILD-TYPE  119  248
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE            2            119
  MALE              4            248
[1] 2 2
[1] FALSE
D84V8, binary
                cls
clus               0   1
  KRAS MUTATED     6   0
  KRAS WILD-TYPE 335   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      6    0
  KRAS WILD-TYPE  335    9
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO             6            335
  YES            0              9
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  KRAS MUTATED                         1                        5
  KRAS WILD-TYPE                       2                      358
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  KRAS MUTATED                                  0
  KRAS WILD-TYPE                                7
D84V9, multiclass
                                  clus
vv                                 KRAS MUTATED KRAS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     1              2
  HEPATOCELLULAR CARCINOMA                    5            358
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  KRAS MUTATED     6   0   0   0
  KRAS WILD-TYPE 321  16   1  22
D84V10, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0            6            321
  R1            0             16
  R2            0              1
  RX            0             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRAS MUTATED                                  0     2
  KRAS WILD-TYPE                                2   158
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED                           0     4
  KRAS WILD-TYPE                        17   180
D84V11, multiclass
                                  clus
vv                                 KRAS MUTATED KRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       2            158
  BLACK OR AFRICAN AMERICAN                   0             17
  WHITE                                       4            180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V12, binary
                cls
clus               0   1
  KRAS MUTATED     0   6
  KRAS WILD-TYPE  18 331
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0    6
  KRAS WILD-TYPE   18  331
                        clus
vv                       KRAS MUTATED KRAS WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            6            331
[1] 2 2
[1] FALSE

Clustering(85) Variable = PGBD1 MUTATION ANALYSIS
D85V1, survival
                 sevent
clus2               0   1
  PGBD1 MUTATED     1   2
  PGBD1 WILD-TYPE 236 128
  PGBD1 MUTATED PGBD1 WILD-TYPE 
              3             364 
  PGBD1 MUTATED PGBD1 WILD-TYPE 
              2             128 
$`PGBD1 MUTATED`
TCGA-DD-A1EE TCGA-G3-A25Y TCGA-G3-A25Z 
       11.47        14.86        21.53 

$`PGBD1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       21.34         9.83        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
        9.14         9.86         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.15        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG 
       79.40        66.31        19.79        75.65        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       27.19        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       30.61        33.14        32.52        21.70        30.97        26.37 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        71.80        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       69.11         0.30         3.52        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV 
       13.64        14.20        59.31        51.35        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       46.82         5.59        47.67         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        42.58        44.22        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.83        13.97        40.47        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       35.67        35.05        34.49        20.91         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       14.89        15.06        14.33        66.67        15.58        18.21 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       19.30        18.25        18.25        18.15        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       19.99         4.64        23.74        15.72        25.08        26.63 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       25.78        50.33        35.08        90.48        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       59.93        72.39        80.71        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        60.99        53.69        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       26.93        28.08        13.91        13.35         9.73         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
       12.82         0.20        14.04        13.15        13.41        13.35 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        1.84         0.20        18.74        19.99        20.61        19.59 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
        0.62        11.93        14.40        60.89        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S 
       27.88        12.03         0.03         0.33         0.39        13.68 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       51.06        53.79        28.27        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        25.25        22.95        24.46        20.42        17.10 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       14.70        20.78        11.87        14.14        15.78        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80        12.23        13.55         0.89        11.64         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        28.90         1.02         2.20         2.99        37.71 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06        16.83        11.80        27.25        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        26.27        17.69        21.01         3.09 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        15.52        36.10        27.88        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        1.71        15.98        10.75        11.34         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       20.22        24.85        18.28        33.86        30.41        22.78 
TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 
       13.55        35.77        25.71        23.21        35.87        25.15 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        45.57        79.30        11.21 

  PGBD1 MUTATED PGBD1 WILD-TYPE 
          11.47            0.03 
  PGBD1 MUTATED PGBD1 WILD-TYPE 
          21.53          120.82 
  PGBD1 MUTATED PGBD1 WILD-TYPE 
         14.860          19.775 
[1] "11.5 - 21.5 (14.9)" "0.0 - 120.8 (19.8)"
[1] "hr=" "2.8"
D85V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PGBD1 MUTATED         2        0         0          1          0          0
  PGBD1 WILD-TYPE     172       86         3         63          9          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  PGBD1 MUTATED          0         0         0
  PGBD1 WILD-TYPE        2         1         2
D85V3, multiclass
            clus
vv           PGBD1 MUTATED PGBD1 WILD-TYPE
  STAGE I                2             172
  STAGE II               0              86
  STAGE III              0               3
  STAGE IIIA             1              63
  STAGE IIIB             0               9
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PGBD1 MUTATED     2   0   1   0
  PGBD1 WILD-TYPE 182  94  78  13
D85V4, multiclass
    clus
vv   PGBD1 MUTATED PGBD1 WILD-TYPE
  T1             2             182
  T2             0              94
  T3             1              78
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V5, binary
                 cls
clus                0   1
  PGBD1 MUTATED     3   0
  PGBD1 WILD-TYPE 251   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGBD1 MUTATED      3    0
  PGBD1 WILD-TYPE  251    4
   clus
vv  PGBD1 MUTATED PGBD1 WILD-TYPE
  0             3             251
  1             0               4
[1] 2 2
[1] FALSE
D85V6, binary
                 cls
clus                0   1
  PGBD1 MUTATED     3   0
  PGBD1 WILD-TYPE 266   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGBD1 MUTATED      3    0
  PGBD1 WILD-TYPE  266    4
   clus
vv  PGBD1 MUTATED PGBD1 WILD-TYPE
  0             3             266
  1             0               4
[1] 2 2
[1] FALSE
D85V7, binary
                 cls
clus                0   1
  PGBD1 MUTATED     1   2
  PGBD1 WILD-TYPE 120 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGBD1 MUTATED      1    2
  PGBD1 WILD-TYPE  120  250
        clus
vv       PGBD1 MUTATED PGBD1 WILD-TYPE
  FEMALE             1             120
  MALE               2             250
[1] 2 2
[1] FALSE
D85V8, binary
                 cls
clus                0   1
  PGBD1 MUTATED     3   0
  PGBD1 WILD-TYPE 338   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGBD1 MUTATED      3    0
  PGBD1 WILD-TYPE  338    9
     clus
vv    PGBD1 MUTATED PGBD1 WILD-TYPE
  NO              3             338
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  PGBD1 MUTATED                         0                        3
  PGBD1 WILD-TYPE                       3                      360
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  PGBD1 MUTATED                                  0
  PGBD1 WILD-TYPE                                7
D85V9, multiclass
                                  clus
vv                                 PGBD1 MUTATED PGBD1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                     3             360
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PGBD1 MUTATED     3   0   0   0
  PGBD1 WILD-TYPE 324  16   1  22
D85V10, multiclass
    clus
vv   PGBD1 MUTATED PGBD1 WILD-TYPE
  R0             3             324
  R1             0              16
  R2             0               1
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PGBD1 MUTATED                                  0     2
  PGBD1 WILD-TYPE                                2   158
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PGBD1 MUTATED                           0     1
  PGBD1 WILD-TYPE                        17   183
D85V11, multiclass
                                  clus
vv                                 PGBD1 MUTATED PGBD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        2             158
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        1             183
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V12, binary
                 cls
clus                0   1
  PGBD1 MUTATED     0   3
  PGBD1 WILD-TYPE  18 334
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGBD1 MUTATED      0    3
  PGBD1 WILD-TYPE   18  334
                        clus
vv                       PGBD1 MUTATED PGBD1 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             3             334
[1] 2 2
[1] FALSE

Clustering(86) Variable = LATS1 MUTATION ANALYSIS
D86V1, survival
                 sevent
clus2               0   1
  LATS1 MUTATED     4   3
  LATS1 WILD-TYPE 233 127
  LATS1 MUTATED LATS1 WILD-TYPE 
              7             360 
  LATS1 MUTATED LATS1 WILD-TYPE 
              3             127 
$`LATS1 MUTATED`
TCGA-DD-AAEG TCGA-CC-A3MB TCGA-DD-A1EG TCGA-DD-A3A0 TCGA-DD-AAEE TCGA-RC-A6M4 
       23.64        10.36        45.11        25.81        26.63         0.72 
TCGA-RC-A6M6 
        0.30 

$`LATS1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.17        21.83        18.90         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        20.81        22.92         1.18         8.55        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        17.10        14.76         1.51 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        14.60        18.48        44.81        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.24         8.22         2.86         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC 
        3.35         7.20         3.32         9.86         9.96        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS 
       12.00        13.12        12.56         8.61         9.14         9.86 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        11.47        12.95        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
        5.62        19.76         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       21.70        30.97        26.37        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        40.08        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        29.52        14.89        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       66.67        15.58        18.21        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 
       18.15        20.98        18.61        19.99         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       15.72        25.08        25.78        50.33        35.08        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       89.69        82.62        59.93        72.39        80.71        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        60.99 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        9.73         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.39        13.68        51.06        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
       22.95        24.46        20.42        17.10        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       11.87        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M5 TCGA-RC-A7S9 
       26.27        17.69        21.01         3.09         0.49        21.04 
TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       19.33        19.04        15.39        15.52        36.10        27.88 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L 
       19.76        16.44         1.71        15.98        10.75        11.34 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD 
        0.99        12.99        20.22        24.85        18.28        33.86 
TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       30.41        22.78        13.55        35.77        25.71        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       35.87        25.15        12.99        45.57        79.30        11.21 

  LATS1 MUTATED LATS1 WILD-TYPE 
           0.30            0.03 
  LATS1 MUTATED LATS1 WILD-TYPE 
          45.11          120.82 
  LATS1 MUTATED LATS1 WILD-TYPE 
          23.64           19.76 
[1] "0.3 - 45.1 (23.6)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.6"
D86V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  LATS1 MUTATED         4        1         0          2          0          0
  LATS1 WILD-TYPE     170       85         3         62          9          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  LATS1 MUTATED          0         0         0
  LATS1 WILD-TYPE        2         1         2
D86V3, multiclass
            clus
vv           LATS1 MUTATED LATS1 WILD-TYPE
  STAGE I                4             170
  STAGE II               1              85
  STAGE III              0               3
  STAGE IIIA             2              62
  STAGE IIIB             0               9
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LATS1 MUTATED     4   1   2   0
  LATS1 WILD-TYPE 180  93  77  13
D86V4, multiclass
    clus
vv   LATS1 MUTATED LATS1 WILD-TYPE
  T1             4             180
  T2             1              93
  T3             2              77
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V5, binary
                 cls
clus                0   1
  LATS1 MUTATED     4   0
  LATS1 WILD-TYPE 250   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LATS1 MUTATED      4    0
  LATS1 WILD-TYPE  250    4
   clus
vv  LATS1 MUTATED LATS1 WILD-TYPE
  0             4             250
  1             0               4
[1] 2 2
[1] FALSE
D86V6, binary
                 cls
clus                0   1
  LATS1 MUTATED     6   0
  LATS1 WILD-TYPE 263   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LATS1 MUTATED      6    0
  LATS1 WILD-TYPE  263    4
   clus
vv  LATS1 MUTATED LATS1 WILD-TYPE
  0             6             263
  1             0               4
[1] 2 2
[1] FALSE
D86V7, binary
                 cls
clus                0   1
  LATS1 MUTATED     2   5
  LATS1 WILD-TYPE 119 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LATS1 MUTATED      2    5
  LATS1 WILD-TYPE  119  247
        clus
vv       LATS1 MUTATED LATS1 WILD-TYPE
  FEMALE             2             119
  MALE               5             247
[1] 2 2
[1] FALSE
D86V8, binary
                 cls
clus                0   1
  LATS1 MUTATED     5   0
  LATS1 WILD-TYPE 336   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LATS1 MUTATED      5    0
  LATS1 WILD-TYPE  336    9
     clus
vv    LATS1 MUTATED LATS1 WILD-TYPE
  NO              5             336
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  LATS1 MUTATED                         0                        7
  LATS1 WILD-TYPE                       3                      356
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  LATS1 MUTATED                                  0
  LATS1 WILD-TYPE                                7
D86V9, multiclass
                                  clus
vv                                 LATS1 MUTATED LATS1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                     7             356
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LATS1 MUTATED     5   2   0   0
  LATS1 WILD-TYPE 322  14   1  22
D86V10, multiclass
    clus
vv   LATS1 MUTATED LATS1 WILD-TYPE
  R0             5             322
  R1             2              14
  R2             0               1
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LATS1 MUTATED                                  0     3
  LATS1 WILD-TYPE                                2   157
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LATS1 MUTATED                           0     4
  LATS1 WILD-TYPE                        17   180
D86V11, multiclass
                                  clus
vv                                 LATS1 MUTATED LATS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        3             157
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        4             180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V12, binary
                 cls
clus                0   1
  LATS1 MUTATED     0   7
  LATS1 WILD-TYPE  18 330
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LATS1 MUTATED      0    7
  LATS1 WILD-TYPE   18  330
                        clus
vv                       LATS1 MUTATED LATS1 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             7             330
[1] 2 2
[1] FALSE

Clustering(87) Variable = KEAP1 MUTATION ANALYSIS
D87V1, survival
                 sevent
clus2               0   1
  KEAP1 MUTATED     9   8
  KEAP1 WILD-TYPE 228 122
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             17             350 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
              8             122 
$`KEAP1 MUTATED`
TCGA-DD-AAE7 TCGA-ES-A2HS TCGA-2Y-A9GS TCGA-2Y-A9GY TCGA-2Y-A9H3 TCGA-BC-A8YO 
       21.17        22.62        23.80        24.89        49.84        18.48 
TCGA-CC-A7IK TCGA-DD-A1EL TCGA-DD-A4NR TCGA-DD-AACB TCGA-DD-AACO TCGA-DD-AACQ 
        8.61        13.64         0.30        76.41        61.68        14.20 
TCGA-DD-AADM TCGA-ED-A4XI TCGA-G3-A3CK TCGA-K7-A5RG TCGA-RC-A6M6 
        0.39        26.93        19.23        17.06         0.30 

$`KEAP1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-FV-A3I1 TCGA-FV-A3R2 
       21.83        18.90        23.64         9.96         8.12         6.38 
TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
       81.73        30.74        22.13        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
        2.14        31.27        12.72        24.56         0.76         7.04 
TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GT 
       10.32        44.02        29.52         0.69        40.80        53.39 
TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 
       63.75        41.79        80.28        27.88       120.82        40.41 
TCGA-2Y-A9H2 TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA 
       56.91        47.74        18.25        20.81        22.92         1.18 
TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C 
        8.55        13.02        10.78        10.59         0.66        17.10 
TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T 
       14.76         1.51        27.91        37.32        10.13        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 
       27.52         2.99        25.32        23.38         1.12        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BD-A2L6 TCGA-BD-A3EP 
       45.93         0.26        22.36        14.60        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IL 
       21.34         9.83        12.00        13.12        12.56         9.14 
TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.86         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65        11.47        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39W 
       49.15         6.02        33.04        18.35        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       33.14        32.52        21.70        30.97        26.37        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       12.26        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       11.41        75.65        55.40        12.53        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU 
       58.16        42.81        13.64        59.31        51.35        51.52 
TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 
       50.33        46.82         5.59        47.67         5.62         4.50 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
       18.54        21.63        42.58        44.22        22.09        40.08 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF 
       40.54        40.83        13.97        40.47        39.52         3.78 
TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADN 
       37.64        35.67        35.05        34.49        20.91        29.52 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       14.89        15.06        14.33        66.67        15.58        18.21 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       19.30        18.25        18.25        18.15        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       19.99         4.64        23.74        15.72        25.08        26.63 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       25.78        50.33        35.08        90.48        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       59.93        72.39        80.71        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        60.99        53.69        29.92 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       28.08        13.91        13.35         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20        14.04        13.15        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        20.61        19.59         0.62 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.53        25.25        22.95        24.46        20.42        17.10 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       14.70        20.78        11.87        14.14        15.78        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80        12.23        13.55         0.89        11.64         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        28.90         1.02         2.20         2.99        37.71 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       58.88        26.27        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.49        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  KEAP1 MUTATED KEAP1 WILD-TYPE 
           0.30            0.03 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
          76.41          120.82 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
         19.230          19.775 
[1] "0.3 - 76.4 (19.2)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.6"
D87V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  KEAP1 MUTATED         7        7         0          1          0          1
  KEAP1 WILD-TYPE     167       79         3         63          9          8
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  KEAP1 MUTATED          0         0         0
  KEAP1 WILD-TYPE        2         1         2
D87V3, multiclass
            clus
vv           KEAP1 MUTATED KEAP1 WILD-TYPE
  STAGE I                7             167
  STAGE II               7              79
  STAGE III              0               3
  STAGE IIIA             1              63
  STAGE IIIB             0               9
  STAGE IIIC             1               8
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KEAP1 MUTATED     7   8   1   1
  KEAP1 WILD-TYPE 177  86  78  12
D87V4, multiclass
    clus
vv   KEAP1 MUTATED KEAP1 WILD-TYPE
  T1             7             177
  T2             8              86
  T3             1              78
  T4             1              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V5, binary
                 cls
clus                0   1
  KEAP1 MUTATED    11   0
  KEAP1 WILD-TYPE 243   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED     11    0
  KEAP1 WILD-TYPE  243    4
   clus
vv  KEAP1 MUTATED KEAP1 WILD-TYPE
  0            11             243
  1             0               4
[1] 2 2
[1] FALSE
D87V6, binary
                 cls
clus                0   1
  KEAP1 MUTATED    12   0
  KEAP1 WILD-TYPE 257   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED     12    0
  KEAP1 WILD-TYPE  257    4
   clus
vv  KEAP1 MUTATED KEAP1 WILD-TYPE
  0            12             257
  1             0               4
[1] 2 2
[1] FALSE
D87V7, binary
                 cls
clus                0   1
  KEAP1 MUTATED     4  13
  KEAP1 WILD-TYPE 117 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED      4   13
  KEAP1 WILD-TYPE  117  239
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  FEMALE             4             117
  MALE              13             239
[1] 2 2
[1] FALSE
D87V8, binary
                 cls
clus                0   1
  KEAP1 MUTATED    15   0
  KEAP1 WILD-TYPE 326   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED     15    0
  KEAP1 WILD-TYPE  326    9
     clus
vv    KEAP1 MUTATED KEAP1 WILD-TYPE
  NO             15             326
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  KEAP1 MUTATED                         0                       17
  KEAP1 WILD-TYPE                       3                      346
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  KEAP1 MUTATED                                  0
  KEAP1 WILD-TYPE                                7
D87V9, multiclass
                                  clus
vv                                 KEAP1 MUTATED KEAP1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                    17             346
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KEAP1 MUTATED    16   1   0   0
  KEAP1 WILD-TYPE 311  15   1  22
D87V10, multiclass
    clus
vv   KEAP1 MUTATED KEAP1 WILD-TYPE
  R0            16             311
  R1             1              15
  R2             0               1
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KEAP1 MUTATED                                  0     8
  KEAP1 WILD-TYPE                                2   152
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KEAP1 MUTATED                           2     7
  KEAP1 WILD-TYPE                        15   177
D87V11, multiclass
                                  clus
vv                                 KEAP1 MUTATED KEAP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        8             152
  BLACK OR AFRICAN AMERICAN                    2              15
  WHITE                                        7             177
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V12, binary
                 cls
clus                0   1
  KEAP1 MUTATED     2  15
  KEAP1 WILD-TYPE  16 322
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED      2   15
  KEAP1 WILD-TYPE   16  322
                        clus
vv                       KEAP1 MUTATED KEAP1 WILD-TYPE
  HISPANIC OR LATINO                 2              16
  NOT HISPANIC OR LATINO            15             322
[1] 2 2
[1] FALSE

Clustering(88) Variable = SENP6 MUTATION ANALYSIS
D88V1, survival
                 sevent
clus2               0   1
  SENP6 MUTATED     5   6
  SENP6 WILD-TYPE 232 124
  SENP6 MUTATED SENP6 WILD-TYPE 
             11             356 
  SENP6 MUTATED SENP6 WILD-TYPE 
              6             124 
$`SENP6 MUTATED`
TCGA-BC-A112 TCGA-G3-A3CG TCGA-5C-A9VG TCGA-CC-A3MA TCGA-DD-A39Y TCGA-DD-A3A7 
        5.03        22.13        10.78         9.96         5.62        13.78 
TCGA-DD-AAC9 TCGA-DD-AACD TCGA-DD-AAEB TCGA-FV-A2QR TCGA-G3-A3CJ 
       11.41        12.53        15.72        19.10        19.53 

$`SENP6 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-K7-A5RF 
        6.38        81.73        30.74        22.06         1.84        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
        2.14        31.27        12.72        24.56         0.76         7.04 
TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
       10.32        44.02        29.52         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
      120.82        40.41        56.91        49.84        47.74        18.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VH 
       20.81        22.92         1.18         8.55        13.02        10.59 
TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q 
        0.66        17.10        14.76         1.51        27.91        37.32 
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       10.13        27.52        27.52         2.99        25.32        23.38 
TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H 
        1.12        44.42        45.93         0.26        22.36        14.60 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 
       18.48        44.81        13.45         0.66         4.24         8.22 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 
        2.86         3.19         3.39         4.24         3.35         7.20 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD 
        3.32         9.86        10.36        11.93        11.41         9.99 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II 
        8.94         7.13        21.34         9.83        12.00        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU 
       12.56         8.61         9.14         9.86         4.60        11.31 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        9.17         6.94         8.15        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.33       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       11.47        12.95        45.11        49.15         6.02        33.04 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Z 
       18.35        13.64        21.14        27.19        55.69        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF 
      107.11        30.61        33.14        32.52        21.70        30.97 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       26.37        30.15        30.51        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       23.93         9.30        23.05        22.78         1.45        35.67 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
      114.35        13.48         0.53        75.65        76.41        55.40 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       71.80        12.00        15.42         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
        0.30         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       14.20        59.31        51.35        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.05        34.49        20.91         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
        4.64        23.74        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        89.69        82.62        59.93        72.39 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        60.99        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        20.61        19.59         0.62        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       14.40        60.89        23.97        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI 
       14.86        21.53        25.64         5.92        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
       22.95        24.46        20.42        17.10        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       11.87        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  SENP6 MUTATED SENP6 WILD-TYPE 
           5.03            0.03 
  SENP6 MUTATED SENP6 WILD-TYPE 
          22.13          120.82 
  SENP6 MUTATED SENP6 WILD-TYPE 
          12.53           20.17 
[1] "5.0 - 22.1 (12.5)"  "0.0 - 120.8 (20.2)"
[1] "hr=" "2.9"
D88V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  SENP6 MUTATED         6        2         0          1          1          0
  SENP6 WILD-TYPE     168       84         3         63          8          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  SENP6 MUTATED          0         0         0
  SENP6 WILD-TYPE        2         1         2
D88V3, multiclass
            clus
vv           SENP6 MUTATED SENP6 WILD-TYPE
  STAGE I                6             168
  STAGE II               2              84
  STAGE III              0               3
  STAGE IIIA             1              63
  STAGE IIIB             1               8
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SENP6 MUTATED     6   2   3   0
  SENP6 WILD-TYPE 178  92  76  13
D88V4, multiclass
    clus
vv   SENP6 MUTATED SENP6 WILD-TYPE
  T1             6             178
  T2             2              92
  T3             3              76
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V5, binary
                 cls
clus                0   1
  SENP6 MUTATED     9   0
  SENP6 WILD-TYPE 245   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP6 MUTATED      9    0
  SENP6 WILD-TYPE  245    4
   clus
vv  SENP6 MUTATED SENP6 WILD-TYPE
  0             9             245
  1             0               4
[1] 2 2
[1] FALSE
D88V6, binary
                 cls
clus                0   1
  SENP6 MUTATED    10   0
  SENP6 WILD-TYPE 259   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP6 MUTATED     10    0
  SENP6 WILD-TYPE  259    4
   clus
vv  SENP6 MUTATED SENP6 WILD-TYPE
  0            10             259
  1             0               4
[1] 2 2
[1] FALSE
D88V7, binary
                 cls
clus                0   1
  SENP6 MUTATED     0  11
  SENP6 WILD-TYPE 121 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP6 MUTATED      0   11
  SENP6 WILD-TYPE  121  241
        clus
vv       SENP6 MUTATED SENP6 WILD-TYPE
  FEMALE             0             121
  MALE              11             241
[1] 2 2
[1] FALSE
D88V8, binary
                 cls
clus                0   1
  SENP6 MUTATED    11   0
  SENP6 WILD-TYPE 330   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP6 MUTATED     11    0
  SENP6 WILD-TYPE  330    9
     clus
vv    SENP6 MUTATED SENP6 WILD-TYPE
  NO             11             330
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  SENP6 MUTATED                         0                       11
  SENP6 WILD-TYPE                       3                      352
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  SENP6 MUTATED                                  0
  SENP6 WILD-TYPE                                7
D88V9, multiclass
                                  clus
vv                                 SENP6 MUTATED SENP6 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                    11             352
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SENP6 MUTATED     9   1   0   1
  SENP6 WILD-TYPE 318  15   1  21
D88V10, multiclass
    clus
vv   SENP6 MUTATED SENP6 WILD-TYPE
  R0             9             318
  R1             1              15
  R2             0               1
  RX             1              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SENP6 MUTATED                                  1     5
  SENP6 WILD-TYPE                                1   155
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SENP6 MUTATED                           0     4
  SENP6 WILD-TYPE                        17   180
D88V11, multiclass
                                  clus
vv                                 SENP6 MUTATED SENP6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               1
  ASIAN                                        5             155
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        4             180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V12, binary
                 cls
clus                0   1
  SENP6 MUTATED     0  10
  SENP6 WILD-TYPE  18 327
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP6 MUTATED      0   10
  SENP6 WILD-TYPE   18  327
                        clus
vv                       SENP6 MUTATED SENP6 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO            10             327
[1] 2 2
[1] FALSE

Clustering(89) Variable = FKBP4 MUTATION ANALYSIS
D89V1, survival
                 sevent
clus2               0   1
  FKBP4 MUTATED     3   1
  FKBP4 WILD-TYPE 234 129
  FKBP4 MUTATED FKBP4 WILD-TYPE 
              4             363 
  FKBP4 MUTATED FKBP4 WILD-TYPE 
              1             129 
$`FKBP4 MUTATED`
TCGA-LG-A6GG TCGA-DD-A3A0 TCGA-G3-A3CJ TCGA-UB-A7MB 
       12.72        25.81        19.53        19.76 

$`FKBP4 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-MI-A75H TCGA-T1-A6J8 
        1.84        20.75         2.14        31.27        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 
       18.25        20.81        22.92         1.18         8.55        13.02 
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM 
       10.78        10.59         0.66        17.10        14.76         1.51 
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        14.60        18.48        44.81        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.24         8.22         2.86         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.35         7.20         3.32         9.86         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
       11.93        11.41         9.99         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        9.83        12.00        13.12        12.56         8.61         9.14 
TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.86         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65        11.47        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       27.19        55.69         5.62        19.76         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       33.14        32.52        21.70        30.97        26.37        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       23.05        22.78         1.45        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        75.65        76.41        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       71.80        12.00        15.42         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
        0.30         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       14.20        59.31        51.35        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.05        34.49        20.91         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        23.74        15.72        25.08        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        90.48        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.39        80.71        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        60.99        53.69        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       28.08        13.91        13.35         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20        14.04        13.15        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        20.61        19.59         0.62 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        14.86        21.53        25.64         5.92 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        25.25        22.95        24.46        20.42        17.10 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       14.70        20.78        11.87        14.14        15.78        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80        12.23        13.55         0.89        11.64         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        28.90         1.02         2.20         2.99        37.71 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06        16.83        11.80        27.25        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        26.27        17.69        21.01         3.09 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD 
       15.39        15.52        36.10        27.88        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        22.78        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        25.71        23.21        35.87        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  FKBP4 MUTATED FKBP4 WILD-TYPE 
          12.72            0.03 
  FKBP4 MUTATED FKBP4 WILD-TYPE 
          25.81          120.82 
  FKBP4 MUTATED FKBP4 WILD-TYPE 
         19.645          19.790 
[1] "12.7 - 25.8 (19.6)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1.1"
D89V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  FKBP4 MUTATED         1        3         0          0          0          0
  FKBP4 WILD-TYPE     173       83         3         64          9          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  FKBP4 MUTATED          0         0         0
  FKBP4 WILD-TYPE        2         1         2
D89V3, multiclass
            clus
vv           FKBP4 MUTATED FKBP4 WILD-TYPE
  STAGE I                1             173
  STAGE II               3              83
  STAGE III              0               3
  STAGE IIIA             0              64
  STAGE IIIB             0               9
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FKBP4 MUTATED     1   3   0   0
  FKBP4 WILD-TYPE 183  91  79  13
D89V4, multiclass
    clus
vv   FKBP4 MUTATED FKBP4 WILD-TYPE
  T1             1             183
  T2             3              91
  T3             0              79
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V5, binary
                 cls
clus                0   1
  FKBP4 MUTATED     1   0
  FKBP4 WILD-TYPE 253   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP4 MUTATED      1    0
  FKBP4 WILD-TYPE  253    4
   clus
vv  FKBP4 MUTATED FKBP4 WILD-TYPE
  0             1             253
  1             0               4
[1] 2 2
[1] FALSE
D89V6, binary
                 cls
clus                0   1
  FKBP4 MUTATED     3   0
  FKBP4 WILD-TYPE 266   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP4 MUTATED      3    0
  FKBP4 WILD-TYPE  266    4
   clus
vv  FKBP4 MUTATED FKBP4 WILD-TYPE
  0             3             266
  1             0               4
[1] 2 2
[1] FALSE
D89V7, binary
                 cls
clus                0   1
  FKBP4 MUTATED     1   3
  FKBP4 WILD-TYPE 120 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP4 MUTATED      1    3
  FKBP4 WILD-TYPE  120  249
        clus
vv       FKBP4 MUTATED FKBP4 WILD-TYPE
  FEMALE             1             120
  MALE               3             249
[1] 2 2
[1] FALSE
D89V8, binary
                 cls
clus                0   1
  FKBP4 MUTATED     4   0
  FKBP4 WILD-TYPE 337   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP4 MUTATED      4    0
  FKBP4 WILD-TYPE  337    9
     clus
vv    FKBP4 MUTATED FKBP4 WILD-TYPE
  NO              4             337
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  FKBP4 MUTATED                         0                        4
  FKBP4 WILD-TYPE                       3                      359
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  FKBP4 MUTATED                                  0
  FKBP4 WILD-TYPE                                7
D89V9, multiclass
                                  clus
vv                                 FKBP4 MUTATED FKBP4 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                     4             359
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FKBP4 MUTATED     4   0   0   0
  FKBP4 WILD-TYPE 323  16   1  22
D89V10, multiclass
    clus
vv   FKBP4 MUTATED FKBP4 WILD-TYPE
  R0             4             323
  R1             0              16
  R2             0               1
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FKBP4 MUTATED                                  1     0
  FKBP4 WILD-TYPE                                1   160
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FKBP4 MUTATED                           0     3
  FKBP4 WILD-TYPE                        17   181
D89V11, multiclass
                                  clus
vv                                 FKBP4 MUTATED FKBP4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               1
  ASIAN                                        0             160
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        3             181
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V12, binary
                 cls
clus                0   1
  FKBP4 MUTATED     0   4
  FKBP4 WILD-TYPE  18 333
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP4 MUTATED      0    4
  FKBP4 WILD-TYPE   18  333
                        clus
vv                       FKBP4 MUTATED FKBP4 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             4             333
[1] 2 2
[1] FALSE

Clustering(90) Variable = FOXK2 MUTATION ANALYSIS
D90V1, survival
                 sevent
clus2               0   1
  FOXK2 MUTATED     2   4
  FOXK2 WILD-TYPE 235 126
  FOXK2 MUTATED FOXK2 WILD-TYPE 
              6             361 
  FOXK2 MUTATED FOXK2 WILD-TYPE 
              4             126 
$`FOXK2 MUTATED`
TCGA-4R-AA8I TCGA-2Y-A9HA TCGA-BC-A69H TCGA-DD-A3A1 TCGA-DD-AAW2 TCGA-G3-AAV4 
        8.61         1.18        14.60         7.66        60.99         0.89 

$`FOXK2 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A5W4 
       83.24        11.74        38.40        69.57         5.03        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       18.25        20.81        22.92         8.55        13.02        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 
       10.59         0.66        17.10        14.76         1.51        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.38         1.12        44.42        45.93         0.26        22.36 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 
       18.48        44.81        13.45         0.66         4.24         8.22 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 
        2.86         3.19         3.39         4.24         3.35         7.20 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC 
        3.32         9.86         9.96        10.36        11.93        11.41 
TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH 
        9.99         8.94         7.13        21.34         9.83        12.00 
TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT 
       13.12        12.56         8.61         9.14         9.86         4.60 
TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 
       11.31         9.17         6.94         8.15        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       75.65        11.47        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
        5.62        19.76        25.81        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       21.70        30.97        26.37        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 
        5.62         4.50        18.54        21.63        42.58        44.22 
TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD 
       22.09        40.08        40.54        40.83        13.97        40.47 
TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       39.52         3.78        37.64        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        29.52        14.89        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 
       66.67        15.58        18.21        19.30        18.25        18.25 
TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 
       18.15        20.98        18.61        19.99         4.64        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       15.72        25.08        26.63        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       90.48        89.69        82.62        59.93        72.39        80.71 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        9.73         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.39        13.68        51.06        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
       22.95        24.46        20.42        17.10        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       11.87        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
       13.55        11.64         2.14        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       27.25        29.79        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       22.95        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       17.69        21.01         3.09         0.72         0.49         0.30 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.04        19.33        19.04        15.39        15.52        36.10 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       27.88        19.76        16.44         1.71        15.98        10.75 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       11.34         0.99        12.99        20.22        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        22.78        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.21        35.87        25.15        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  FOXK2 MUTATED FOXK2 WILD-TYPE 
           0.89            0.03 
  FOXK2 MUTATED FOXK2 WILD-TYPE 
          60.99          120.82 
  FOXK2 MUTATED FOXK2 WILD-TYPE 
          8.135          19.990 
[1] "0.9 - 61.0 (8.1)"   "0.0 - 120.8 (20.0)"
[1] "hr=" "3.3"
D90V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  FOXK2 MUTATED         2        3         0          1          0          0
  FOXK2 WILD-TYPE     172       83         3         63          9          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  FOXK2 MUTATED          0         0         0
  FOXK2 WILD-TYPE        2         1         2
D90V3, multiclass
            clus
vv           FOXK2 MUTATED FOXK2 WILD-TYPE
  STAGE I                2             172
  STAGE II               3              83
  STAGE III              0               3
  STAGE IIIA             1              63
  STAGE IIIB             0               9
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FOXK2 MUTATED     2   3   1   0
  FOXK2 WILD-TYPE 182  91  78  13
D90V4, multiclass
    clus
vv   FOXK2 MUTATED FOXK2 WILD-TYPE
  T1             2             182
  T2             3              91
  T3             1              78
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V5, binary
                 cls
clus                0   1
  FOXK2 MUTATED     3   0
  FOXK2 WILD-TYPE 251   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXK2 MUTATED      3    0
  FOXK2 WILD-TYPE  251    4
   clus
vv  FOXK2 MUTATED FOXK2 WILD-TYPE
  0             3             251
  1             0               4
[1] 2 2
[1] FALSE
D90V6, binary
                 cls
clus                0   1
  FOXK2 MUTATED     4   0
  FOXK2 WILD-TYPE 265   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXK2 MUTATED      4    0
  FOXK2 WILD-TYPE  265    4
   clus
vv  FOXK2 MUTATED FOXK2 WILD-TYPE
  0             4             265
  1             0               4
[1] 2 2
[1] FALSE
D90V7, binary
                 cls
clus                0   1
  FOXK2 MUTATED     1   5
  FOXK2 WILD-TYPE 120 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXK2 MUTATED      1    5
  FOXK2 WILD-TYPE  120  247
        clus
vv       FOXK2 MUTATED FOXK2 WILD-TYPE
  FEMALE             1             120
  MALE               5             247
[1] 2 2
[1] FALSE
D90V8, binary
                 cls
clus                0   1
  FOXK2 MUTATED     6   0
  FOXK2 WILD-TYPE 335   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXK2 MUTATED      6    0
  FOXK2 WILD-TYPE  335    9
     clus
vv    FOXK2 MUTATED FOXK2 WILD-TYPE
  NO              6             335
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  FOXK2 MUTATED                         0                        6
  FOXK2 WILD-TYPE                       3                      357
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  FOXK2 MUTATED                                  0
  FOXK2 WILD-TYPE                                7
D90V9, multiclass
                                  clus
vv                                 FOXK2 MUTATED FOXK2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                     6             357
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FOXK2 MUTATED     6   0   0   0
  FOXK2 WILD-TYPE 321  16   1  22
D90V10, multiclass
    clus
vv   FOXK2 MUTATED FOXK2 WILD-TYPE
  R0             6             321
  R1             0              16
  R2             0               1
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FOXK2 MUTATED                                  0     1
  FOXK2 WILD-TYPE                                2   159
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FOXK2 MUTATED                           0     4
  FOXK2 WILD-TYPE                        17   180
D90V11, multiclass
                                  clus
vv                                 FOXK2 MUTATED FOXK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1             159
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        4             180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V12, binary
                 cls
clus                0   1
  FOXK2 MUTATED     0   5
  FOXK2 WILD-TYPE  18 332
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXK2 MUTATED      0    5
  FOXK2 WILD-TYPE   18  332
                        clus
vv                       FOXK2 MUTATED FOXK2 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             5             332
[1] 2 2
[1] FALSE

Clustering(91) Variable = DSPP MUTATION ANALYSIS
D91V1, survival
                sevent
clus2              0   1
  DSPP MUTATED    14   6
  DSPP WILD-TYPE 223 124
  DSPP MUTATED DSPP WILD-TYPE 
            20            347 
  DSPP MUTATED DSPP WILD-TYPE 
             6            124 
$`DSPP MUTATED`
TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-BC-A3KF TCGA-BD-A3EP TCGA-DD-A1EH TCGA-DD-A73G 
       22.06         1.84         0.26        13.45        49.15       114.35 
TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACI TCGA-DD-AADG TCGA-DD-AADU TCGA-FV-A2QQ 
       55.40        12.53        53.19        37.64        18.21        23.97 
TCGA-HP-A5MZ TCGA-MI-A75G TCGA-RG-A7D4 TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
        2.99        22.95        36.10        13.55        35.77        25.71 
TCGA-ZP-A9D0 TCGA-ZS-A9CG 
       35.87        11.21 

$`DSPP WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-K7-A5RF 
        8.12         6.38        81.73        30.74        22.13        20.75 
TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 TCGA-UB-A7MF 
        2.14        31.27        12.72        24.56         0.76         7.04 
TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-2Y-A9GS 
       10.32        44.02        29.52         0.69        40.80        23.80 
TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY TCGA-2Y-A9GZ 
       53.39        63.75        41.79        80.28        24.89        27.88 
TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 TCGA-2Y-A9H5 
      120.82        40.41        56.91        49.84        47.74        18.25 
TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       20.81        22.92         1.18         8.55        13.02        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 
       10.59         0.66        17.10        14.76         1.51        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A69H 
       23.38         1.12        44.42        45.93        22.36        14.60 
TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 
       18.48        44.81         0.66         4.24         8.22         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT 
        3.19         3.39         4.24         3.35         7.20         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD 
        9.86         9.96        10.36        11.93        11.41         9.99 
TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II 
        8.94         7.13        21.34         9.83        12.00        13.12 
TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU 
       12.56         8.61         9.14         9.86         4.60        11.31 
TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        9.17         6.94         8.15        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.33       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       11.47        12.95        45.11         6.02        33.04        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       13.64        21.14        27.19        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE 
      107.11        13.78        30.61        33.14        32.52        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        26.37        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        23.93         9.30        23.05        22.78         1.45 
TCGA-DD-A73F TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB 
       35.67        13.48         0.53        11.41        75.65        76.41 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACJ TCGA-DD-AACK 
       71.80        12.00        15.42         6.41        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK 
       40.47        39.52         3.78        35.67        35.05        34.49 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ 
       20.91         0.39        29.52        14.89        15.06        14.33 
TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 
       66.67        15.58        19.30        18.25        18.25        18.15 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB 
       20.98        18.61        19.99         4.64        23.74        15.72 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP 
       25.08        26.63        25.78        50.33        35.08        90.48 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW 
       89.69        82.62        59.93        72.39        80.71        76.18 
TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 
       56.48        64.77        62.47        66.25        65.39        60.99 
TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       53.69        29.92        26.93        28.08        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        9.73         0.20        12.82         0.20        14.04        13.15 
TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S 
       13.41        13.35         1.84         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ 
       19.10        27.88        12.03         0.03         0.33         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z 
       13.68        51.06        53.79        28.27        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        25.25        22.95 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       24.46        20.42        17.10        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        0.89        11.64         2.14        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 
        2.20        37.71        17.06        16.83        11.80        27.25 
TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I 
       29.79        13.97        12.03         9.57        16.67        20.71 
TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
        7.53        10.85        58.88        26.27        17.69        21.01 
TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB 
        3.09         0.72         0.49         0.30        21.04        19.33 
TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       19.04        15.39        15.52        27.88        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        1.71        15.98        10.75        11.34         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       20.22        24.85        18.28        33.86        30.41        22.78 
TCGA-ZP-A9CZ TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.21        25.15        12.99        45.57        79.30 

  DSPP MUTATED DSPP WILD-TYPE 
          0.26           0.03 
  DSPP MUTATED DSPP WILD-TYPE 
        114.35         120.82 
  DSPP MUTATED DSPP WILD-TYPE 
         23.46          19.59 
[1] "0.3 - 114.3 (23.5)" "0.0 - 120.8 (19.6)"
[1] "hr=" "1.3"
D91V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DSPP MUTATED         7        5         1          3          2          0
  DSPP WILD-TYPE     167       81         2         61          7          9
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  DSPP MUTATED          0         0         0
  DSPP WILD-TYPE        2         1         2
D91V3, multiclass
            clus
vv           DSPP MUTATED DSPP WILD-TYPE
  STAGE I               7            167
  STAGE II              5             81
  STAGE III             1              2
  STAGE IIIA            3             61
  STAGE IIIB            2              7
  STAGE IIIC            0              9
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DSPP MUTATED    10   5   6   0
  DSPP WILD-TYPE 174  89  73  13
D91V4, multiclass
    clus
vv   DSPP MUTATED DSPP WILD-TYPE
  T1           10            174
  T2            5             89
  T3            6             73
  T4            0             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V5, binary
                cls
clus               0   1
  DSPP MUTATED    14   0
  DSPP WILD-TYPE 240   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSPP MUTATED     14    0
  DSPP WILD-TYPE  240    4
   clus
vv  DSPP MUTATED DSPP WILD-TYPE
  0           14            240
  1            0              4
[1] 2 2
[1] FALSE
D91V6, binary
                cls
clus               0   1
  DSPP MUTATED    14   0
  DSPP WILD-TYPE 255   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSPP MUTATED     14    0
  DSPP WILD-TYPE  255    4
   clus
vv  DSPP MUTATED DSPP WILD-TYPE
  0           14            255
  1            0              4
[1] 2 2
[1] FALSE
D91V7, binary
                cls
clus               0   1
  DSPP MUTATED     6  15
  DSPP WILD-TYPE 115 237
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSPP MUTATED      6   15
  DSPP WILD-TYPE  115  237
        clus
vv       DSPP MUTATED DSPP WILD-TYPE
  FEMALE            6            115
  MALE             15            237
[1] 2 2
[1] FALSE
D91V8, binary
                cls
clus               0   1
  DSPP MUTATED    19   0
  DSPP WILD-TYPE 322   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSPP MUTATED     19    0
  DSPP WILD-TYPE  322    9
     clus
vv    DSPP MUTATED DSPP WILD-TYPE
  NO            19            322
  YES            0              9
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  DSPP MUTATED                         0                       21
  DSPP WILD-TYPE                       3                      342
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DSPP MUTATED                                  0
  DSPP WILD-TYPE                                7
D91V9, multiclass
                                  clus
vv                                 DSPP MUTATED DSPP WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              3
  HEPATOCELLULAR CARCINOMA                   21            342
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  DSPP MUTATED    21   0   0   0
  DSPP WILD-TYPE 306  16   1  22
D91V10, multiclass
    clus
vv   DSPP MUTATED DSPP WILD-TYPE
  R0           21            306
  R1            0             16
  R2            0              1
  RX            0             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DSPP MUTATED                                  0     6
  DSPP WILD-TYPE                                2   154
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DSPP MUTATED                           3    11
  DSPP WILD-TYPE                        14   173
D91V11, multiclass
                                  clus
vv                                 DSPP MUTATED DSPP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       6            154
  BLACK OR AFRICAN AMERICAN                   3             14
  WHITE                                      11            173
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V12, binary
                cls
clus               0   1
  DSPP MUTATED     1  18
  DSPP WILD-TYPE  17 319
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSPP MUTATED      1   18
  DSPP WILD-TYPE   17  319
                        clus
vv                       DSPP MUTATED DSPP WILD-TYPE
  HISPANIC OR LATINO                1             17
  NOT HISPANIC OR LATINO           18            319
[1] 2 2
[1] FALSE

Clustering(92) Variable = C10ORF28 MUTATION ANALYSIS
D92V1, survival
                    sevent
clus2                  0   1
  C10ORF28 MUTATED     2   2
  C10ORF28 WILD-TYPE 235 128
  C10ORF28 MUTATED C10ORF28 WILD-TYPE 
                 4                363 
  C10ORF28 MUTATED C10ORF28 WILD-TYPE 
                 2                128 
$`C10ORF28 MUTATED`
TCGA-CC-A3MB TCGA-DD-A1EG TCGA-DD-AAEK TCGA-RC-A7SH 
       10.36        45.11        35.08        15.39 

$`C10ORF28 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF 
       11.93        11.41         9.99         8.94         7.13        21.34 
TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
        9.83        12.00        13.12        12.56         8.61         9.14 
TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.86         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EH 
       66.31        19.79        75.65        11.47        12.95        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       33.14        32.52        21.70        30.97        26.37        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       23.05        22.78         1.45        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        75.65        76.41        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       71.80        12.00        15.42         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
        0.30         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       14.20        59.31        51.35        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.05        34.49        20.91         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        23.74        15.72        25.08        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       50.33        90.48        89.69        82.62        59.93        72.39 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        60.99        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK 
       18.74        19.99        20.61        19.59         0.62        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 
       14.40        60.89        23.97        19.10        27.88        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.03         0.33         0.39        13.68        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       28.27        14.86        21.53        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        25.25        22.95        24.46        20.42        17.10 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       14.70        20.78        11.87        14.14        15.78        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80        12.23        13.55         0.89        11.64         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
       11.87        28.90         1.02         2.20         2.99        37.71 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06        16.83        11.80        27.25        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        26.27        17.69        21.01         3.09 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        22.78        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        25.71        23.21        35.87        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  C10ORF28 MUTATED C10ORF28 WILD-TYPE 
             10.36               0.03 
  C10ORF28 MUTATED C10ORF28 WILD-TYPE 
             45.11             120.82 
  C10ORF28 MUTATED C10ORF28 WILD-TYPE 
            25.235             19.760 
[1] "10.4 - 45.1 (25.2)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1.4"
D92V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  C10ORF28 MUTATED         1        2         0          1          0
  C10ORF28 WILD-TYPE     173       84         3         63          9
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  C10ORF28 MUTATED            0        0         0         0
  C10ORF28 WILD-TYPE          9        2         1         2
D92V3, multiclass
            clus
vv           C10ORF28 MUTATED C10ORF28 WILD-TYPE
  STAGE I                   1                173
  STAGE II                  2                 84
  STAGE III                 0                  3
  STAGE IIIA                1                 63
  STAGE IIIB                0                  9
  STAGE IIIC                0                  9
  STAGE IV                  0                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C10ORF28 MUTATED     1   2   1   0
  C10ORF28 WILD-TYPE 183  92  78  13
D92V4, multiclass
    clus
vv   C10ORF28 MUTATED C10ORF28 WILD-TYPE
  T1                1                183
  T2                2                 92
  T3                1                 78
  T4                0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V5, binary
                    cls
clus                   0   1
  C10ORF28 MUTATED     4   0
  C10ORF28 WILD-TYPE 250   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF28 MUTATED      4    0
  C10ORF28 WILD-TYPE  250    4
   clus
vv  C10ORF28 MUTATED C10ORF28 WILD-TYPE
  0                4                250
  1                0                  4
[1] 2 2
[1] FALSE
D92V6, binary
                    cls
clus                   0   1
  C10ORF28 MUTATED     4   0
  C10ORF28 WILD-TYPE 265   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF28 MUTATED      4    0
  C10ORF28 WILD-TYPE  265    4
   clus
vv  C10ORF28 MUTATED C10ORF28 WILD-TYPE
  0                4                265
  1                0                  4
[1] 2 2
[1] FALSE
D92V7, binary
                    cls
clus                   0   1
  C10ORF28 MUTATED     0   4
  C10ORF28 WILD-TYPE 121 248
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF28 MUTATED      0    4
  C10ORF28 WILD-TYPE  121  248
        clus
vv       C10ORF28 MUTATED C10ORF28 WILD-TYPE
  FEMALE                0                121
  MALE                  4                248
[1] 2 2
[1] FALSE
D92V8, binary
                    cls
clus                   0   1
  C10ORF28 MUTATED     4   0
  C10ORF28 WILD-TYPE 337   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF28 MUTATED      4    0
  C10ORF28 WILD-TYPE  337    9
     clus
vv    C10ORF28 MUTATED C10ORF28 WILD-TYPE
  NO                 4                337
  YES                0                  9
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  C10ORF28 MUTATED                         0                        4
  C10ORF28 WILD-TYPE                       3                      359
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  C10ORF28 MUTATED                                  0
  C10ORF28 WILD-TYPE                                7
D92V9, multiclass
                                  clus
vv                                 C10ORF28 MUTATED C10ORF28 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  3
  HEPATOCELLULAR CARCINOMA                        4                359
  HEPATOCHOLANGIOCARCINOMA (MIXED)                0                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C10ORF28 MUTATED     4   0   0   0
  C10ORF28 WILD-TYPE 323  16   1  22
D92V10, multiclass
    clus
vv   C10ORF28 MUTATED C10ORF28 WILD-TYPE
  R0                4                323
  R1                0                 16
  R2                0                  1
  RX                0                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C10ORF28 MUTATED                                  0     3
  C10ORF28 WILD-TYPE                                2   157
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C10ORF28 MUTATED                           0     1
  C10ORF28 WILD-TYPE                        17   183
D92V11, multiclass
                                  clus
vv                                 C10ORF28 MUTATED C10ORF28 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           3                157
  BLACK OR AFRICAN AMERICAN                       0                 17
  WHITE                                           1                183
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V12, binary
                    cls
clus                   0   1
  C10ORF28 MUTATED     0   4
  C10ORF28 WILD-TYPE  18 333
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF28 MUTATED      0    4
  C10ORF28 WILD-TYPE   18  333
                        clus
vv                       C10ORF28 MUTATED C10ORF28 WILD-TYPE
  HISPANIC OR LATINO                    0                 18
  NOT HISPANIC OR LATINO                4                333
[1] 2 2
[1] FALSE

Clustering(93) Variable = PRAMEF4 MUTATION ANALYSIS
D93V1, survival
                   sevent
clus2                 0   1
  PRAMEF4 MUTATED     1   3
  PRAMEF4 WILD-TYPE 236 127
  PRAMEF4 MUTATED PRAMEF4 WILD-TYPE 
                4               363 
  PRAMEF4 MUTATED PRAMEF4 WILD-TYPE 
                3               127 
$`PRAMEF4 MUTATED`
TCGA-CC-A7IH TCGA-DD-A39Z TCGA-GJ-A6C0 TCGA-YA-A8S7 
       12.00        19.76         1.02        13.55 

$`PRAMEF4 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL 
       21.34         9.83        13.12        12.56         8.61         9.14 
TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW 
        9.86         4.60        11.31         9.17         6.94         8.15 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65        11.47        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       27.19        55.69         5.62        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       33.14        32.52        21.70        30.97        26.37        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       23.05        22.78         1.45        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        75.65        76.41        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       71.80        12.00        15.42         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
        0.30         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       14.20        59.31        51.35        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.05        34.49        20.91         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        23.74        15.72        25.08        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        90.48        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.39        80.71        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        60.99        53.69        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       28.08        13.91        13.35         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20        14.04        13.15        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        20.61        19.59         0.62 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       19.53        19.23        25.25        22.95        24.46        20.42 
TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       17.10        14.70        20.78        11.87        14.14        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.65        11.80        12.23        13.55         0.89        11.64 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 
        2.14        11.87        28.90         2.20         2.99        37.71 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC 
       17.06        16.83        11.80        27.25        29.79        13.97 
TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 
       12.03         9.57        16.67        22.95        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        26.27        17.69        21.01         3.09 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       15.39        15.52        36.10        27.88        19.76        16.44 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B 
        1.71        15.98        10.75        11.34         0.99        12.99 
TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF 
       20.22        24.85        18.28        33.86        30.41        22.78 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        25.71        23.21        35.87        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  PRAMEF4 MUTATED PRAMEF4 WILD-TYPE 
             1.02              0.03 
  PRAMEF4 MUTATED PRAMEF4 WILD-TYPE 
            19.76            120.82 
  PRAMEF4 MUTATED PRAMEF4 WILD-TYPE 
           12.775            19.990 
[1] "1.0 - 19.8 (12.8)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "4.4"
D93V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PRAMEF4 MUTATED         0        2         0          2          0          0
  PRAMEF4 WILD-TYPE     174       84         3         62          9          9
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  PRAMEF4 MUTATED          0         0         0
  PRAMEF4 WILD-TYPE        2         1         2
D93V3, multiclass
            clus
vv           PRAMEF4 MUTATED PRAMEF4 WILD-TYPE
  STAGE I                  0               174
  STAGE II                 2                84
  STAGE III                0                 3
  STAGE IIIA               2                62
  STAGE IIIB               0                 9
  STAGE IIIC               0                 9
  STAGE IV                 0                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PRAMEF4 MUTATED     0   2   2   0
  PRAMEF4 WILD-TYPE 184  92  77  13
D93V4, multiclass
    clus
vv   PRAMEF4 MUTATED PRAMEF4 WILD-TYPE
  T1               0               184
  T2               2                92
  T3               2                77
  T4               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V5, binary
                   cls
clus                  0   1
  PRAMEF4 MUTATED     2   0
  PRAMEF4 WILD-TYPE 252   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRAMEF4 MUTATED      2    0
  PRAMEF4 WILD-TYPE  252    4
   clus
vv  PRAMEF4 MUTATED PRAMEF4 WILD-TYPE
  0               2               252
  1               0                 4
[1] 2 2
[1] FALSE
D93V6, binary
                   cls
clus                  0   1
  PRAMEF4 MUTATED     2   0
  PRAMEF4 WILD-TYPE 267   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRAMEF4 MUTATED      2    0
  PRAMEF4 WILD-TYPE  267    4
   clus
vv  PRAMEF4 MUTATED PRAMEF4 WILD-TYPE
  0               2               267
  1               0                 4
[1] 2 2
[1] FALSE
D93V7, binary
                   cls
clus                  0   1
  PRAMEF4 MUTATED     2   2
  PRAMEF4 WILD-TYPE 119 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRAMEF4 MUTATED      2    2
  PRAMEF4 WILD-TYPE  119  250
        clus
vv       PRAMEF4 MUTATED PRAMEF4 WILD-TYPE
  FEMALE               2               119
  MALE                 2               250
[1] 2 2
[1] FALSE
D93V8, binary
                   cls
clus                  0   1
  PRAMEF4 MUTATED     3   0
  PRAMEF4 WILD-TYPE 338   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRAMEF4 MUTATED      3    0
  PRAMEF4 WILD-TYPE  338    9
     clus
vv    PRAMEF4 MUTATED PRAMEF4 WILD-TYPE
  NO                3               338
  YES               0                 9
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  PRAMEF4 MUTATED                         0                        4
  PRAMEF4 WILD-TYPE                       3                      359
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  PRAMEF4 MUTATED                                  0
  PRAMEF4 WILD-TYPE                                7
D93V9, multiclass
                                  clus
vv                                 PRAMEF4 MUTATED PRAMEF4 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 3
  HEPATOCELLULAR CARCINOMA                       4               359
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PRAMEF4 MUTATED     3   0   0   1
  PRAMEF4 WILD-TYPE 324  16   1  21
D93V10, multiclass
    clus
vv   PRAMEF4 MUTATED PRAMEF4 WILD-TYPE
  R0               3               324
  R1               0                16
  R2               0                 1
  RX               1                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRAMEF4 MUTATED                                  0     1
  PRAMEF4 WILD-TYPE                                2   159
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PRAMEF4 MUTATED                           0     2
  PRAMEF4 WILD-TYPE                        17   182
D93V11, multiclass
                                  clus
vv                                 PRAMEF4 MUTATED PRAMEF4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1               159
  BLACK OR AFRICAN AMERICAN                      0                17
  WHITE                                          2               182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V12, binary
                   cls
clus                  0   1
  PRAMEF4 MUTATED     1   2
  PRAMEF4 WILD-TYPE  17 335
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRAMEF4 MUTATED      1    2
  PRAMEF4 WILD-TYPE   17  335
                        clus
vv                       PRAMEF4 MUTATED PRAMEF4 WILD-TYPE
  HISPANIC OR LATINO                   1                17
  NOT HISPANIC OR LATINO               2               335
[1] 2 2
[1] FALSE

Clustering(94) Variable = RPS6KA5 MUTATION ANALYSIS
D94V1, survival
                   sevent
clus2                 0   1
  RPS6KA5 MUTATED     3   2
  RPS6KA5 WILD-TYPE 234 128
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
                5               362 
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
                2               128 
$`RPS6KA5 MUTATED`
TCGA-DD-A1EE TCGA-DD-A3A1 TCGA-DD-AACT TCGA-DD-AAE6 TCGA-EP-A26S 
       11.47         7.66        51.35         4.64        19.99 

$`RPS6KA5 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       21.34         9.83        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
        9.14         9.86         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.15        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG 
       79.40        66.31        19.79        75.65        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 
       27.19        55.69         5.62        19.76        25.81        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       33.14        32.52        21.70        30.97        26.37        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       23.05        22.78         1.45        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        75.65        76.41        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       71.80        12.00        15.42         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
        0.30         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       14.20        59.31        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       34.49        20.91         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
       14.33        66.67        15.58        18.21        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE9 
       18.25        18.15        20.98        18.61        19.99        23.74 
TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK 
       15.72        25.08        26.63        25.78        50.33        35.08 
TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV 
       90.48        89.69        82.62        59.93        72.39        80.71 
TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 
       76.18        56.48        64.77        62.47        66.25        65.39 
TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       60.99        53.69        29.92        26.93        28.08        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         9.73         0.20        12.82         0.20        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       13.15        13.41        13.35         1.84         0.20        18.74 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B 
       20.61        19.59         0.62        11.93        14.40        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.39        13.68        51.06        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
       22.95        24.46        20.42        17.10        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       11.87        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
             4.64              0.03 
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
            51.35            120.82 
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
           11.470            19.775 
[1] "4.6 - 51.4 (11.5)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "1.6"
D94V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  RPS6KA5 MUTATED         3        0         0          2          0          0
  RPS6KA5 WILD-TYPE     171       86         3         62          9          9
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  RPS6KA5 MUTATED          0         0         0
  RPS6KA5 WILD-TYPE        2         1         2
D94V3, multiclass
            clus
vv           RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  STAGE I                  3               171
  STAGE II                 0                86
  STAGE III                0                 3
  STAGE IIIA               2                62
  STAGE IIIB               0                 9
  STAGE IIIC               0                 9
  STAGE IV                 0                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RPS6KA5 MUTATED     3   0   2   0
  RPS6KA5 WILD-TYPE 181  94  77  13
D94V4, multiclass
    clus
vv   RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  T1               3               181
  T2               0                94
  T3               2                77
  T4               0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V5, binary
                   cls
clus                  0   1
  RPS6KA5 MUTATED     5   0
  RPS6KA5 WILD-TYPE 249   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA5 MUTATED      5    0
  RPS6KA5 WILD-TYPE  249    4
   clus
vv  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  0               5               249
  1               0                 4
[1] 2 2
[1] FALSE
D94V6, binary
                   cls
clus                  0   1
  RPS6KA5 MUTATED     4   0
  RPS6KA5 WILD-TYPE 265   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA5 MUTATED      4    0
  RPS6KA5 WILD-TYPE  265    4
   clus
vv  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  0               4               265
  1               0                 4
[1] 2 2
[1] FALSE
D94V7, binary
                   cls
clus                  0   1
  RPS6KA5 MUTATED     2   3
  RPS6KA5 WILD-TYPE 119 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA5 MUTATED      2    3
  RPS6KA5 WILD-TYPE  119  249
        clus
vv       RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  FEMALE               2               119
  MALE                 3               249
[1] 2 2
[1] FALSE
D94V8, binary
                   cls
clus                  0   1
  RPS6KA5 MUTATED     5   0
  RPS6KA5 WILD-TYPE 336   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA5 MUTATED      5    0
  RPS6KA5 WILD-TYPE  336    9
     clus
vv    RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  NO                5               336
  YES               0                 9
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  RPS6KA5 MUTATED                         0                        5
  RPS6KA5 WILD-TYPE                       3                      358
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  RPS6KA5 MUTATED                                  0
  RPS6KA5 WILD-TYPE                                7
D94V9, multiclass
                                  clus
vv                                 RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 3
  HEPATOCELLULAR CARCINOMA                       5               358
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  RPS6KA5 MUTATED     4   0   0   0
  RPS6KA5 WILD-TYPE 323  16   1  22
D94V10, multiclass
    clus
vv   RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  R0               4               323
  R1               0                16
  R2               0                 1
  RX               0                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPS6KA5 MUTATED                                  0     2
  RPS6KA5 WILD-TYPE                                2   158
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  RPS6KA5 MUTATED                           0     2
  RPS6KA5 WILD-TYPE                        17   182
D94V11, multiclass
                                  clus
vv                                 RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2               158
  BLACK OR AFRICAN AMERICAN                      0                17
  WHITE                                          2               182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V12, binary
                   cls
clus                  0   1
  RPS6KA5 MUTATED     0   4
  RPS6KA5 WILD-TYPE  18 333
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA5 MUTATED      0    4
  RPS6KA5 WILD-TYPE   18  333
                        clus
vv                       RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO               4               333
[1] 2 2
[1] FALSE

Clustering(95) Variable = DDX42 MUTATION ANALYSIS
D95V1, survival
                 sevent
clus2               0   1
  DDX42 MUTATED     2   4
  DDX42 WILD-TYPE 235 126
  DDX42 MUTATED DDX42 WILD-TYPE 
              6             361 
  DDX42 MUTATED DDX42 WILD-TYPE 
              4             126 
$`DDX42 MUTATED`
TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-AACZ TCGA-EP-A2KA TCGA-G3-A25Z TCGA-G3-A5SL 
       11.47        45.11         5.62        20.61        21.53        20.42 

$`DDX42 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       21.34         9.83        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
        9.14         9.86         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.15        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH 
       79.40        66.31        19.79        75.65        12.95        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11        13.78        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       33.14        32.52        21.70        30.97        26.37        30.15 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        78.84        23.93         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A 
       23.05        22.78         1.45        35.67       114.35        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        75.65        76.41        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       71.80        12.00        15.42         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
        0.30         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       14.20        59.31        51.35        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
        5.59        47.67         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       34.49        20.91         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
       14.33        66.67        15.58        18.21        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        89.69        82.62        59.93        72.39 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        60.99        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         9.73         0.20        12.82         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K 
       14.04        13.15        13.41        13.35         1.84         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT 
       18.74        19.99        19.59         0.62        11.93        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 
       60.89        23.97        19.10        27.88        12.03         0.03 
TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33         0.39        13.68        51.06        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       14.86        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
       22.95        24.46        17.10        14.70        20.78        11.87 
TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 
       14.14        15.78        15.65        11.80        12.23        13.55 
TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 
        0.89        11.64         2.14        11.87        28.90         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 
        2.20         2.99        37.71        17.06        16.83        11.80 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       27.25        29.79        13.97        12.03         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF 
       22.95        20.71         7.53        10.85        58.88        26.27 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 
       17.69        21.01         3.09         0.72         0.49         0.30 
TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
       21.04        19.33        19.04        15.39        15.52        36.10 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-AA0U 
       27.88        19.76        16.44         1.71        15.98        10.75 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 TCGA-WX-AA47 
       11.34         0.99        12.99        20.22        24.85        18.28 
TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9CY 
       33.86        30.41        22.78        13.55        35.77        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CF 
       23.21        35.87        25.15        12.99        45.57        79.30 
TCGA-ZS-A9CG 
       11.21 

  DDX42 MUTATED DDX42 WILD-TYPE 
           5.62            0.03 
  DDX42 MUTATED DDX42 WILD-TYPE 
          45.11          120.82 
  DDX42 MUTATED DDX42 WILD-TYPE 
         20.515          19.760 
[1] "5.6 - 45.1 (20.5)"  "0.0 - 120.8 (19.8)"
[1] "hr=" "2.4"
D95V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DDX42 MUTATED         3        1         0          2          0          0
  DDX42 WILD-TYPE     171       85         3         62          9          9
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  DDX42 MUTATED          0         0         0
  DDX42 WILD-TYPE        2         1         2
D95V3, multiclass
            clus
vv           DDX42 MUTATED DDX42 WILD-TYPE
  STAGE I                3             171
  STAGE II               1              85
  STAGE III              0               3
  STAGE IIIA             2              62
  STAGE IIIB             0               9
  STAGE IIIC             0               9
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DDX42 MUTATED     3   1   2   0
  DDX42 WILD-TYPE 181  93  77  13
D95V4, multiclass
    clus
vv   DDX42 MUTATED DDX42 WILD-TYPE
  T1             3             181
  T2             1              93
  T3             2              77
  T4             0              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V5, binary
                 cls
clus                0   1
  DDX42 MUTATED     4   0
  DDX42 WILD-TYPE 250   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX42 MUTATED      4    0
  DDX42 WILD-TYPE  250    4
   clus
vv  DDX42 MUTATED DDX42 WILD-TYPE
  0             4             250
  1             0               4
[1] 2 2
[1] FALSE
D95V6, binary
                 cls
clus                0   1
  DDX42 MUTATED     5   0
  DDX42 WILD-TYPE 264   4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX42 MUTATED      5    0
  DDX42 WILD-TYPE  264    4
   clus
vv  DDX42 MUTATED DDX42 WILD-TYPE
  0             5             264
  1             0               4
[1] 2 2
[1] FALSE
D95V7, binary
                 cls
clus                0   1
  DDX42 MUTATED     2   4
  DDX42 WILD-TYPE 119 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX42 MUTATED      2    4
  DDX42 WILD-TYPE  119  248
        clus
vv       DDX42 MUTATED DDX42 WILD-TYPE
  FEMALE             2             119
  MALE               4             248
[1] 2 2
[1] FALSE
D95V8, binary
                 cls
clus                0   1
  DDX42 MUTATED     6   0
  DDX42 WILD-TYPE 335   9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX42 MUTATED      6    0
  DDX42 WILD-TYPE  335    9
     clus
vv    DDX42 MUTATED DDX42 WILD-TYPE
  NO              6             335
  YES             0               9
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  DDX42 MUTATED                         0                        6
  DDX42 WILD-TYPE                       3                      357
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  DDX42 MUTATED                                  0
  DDX42 WILD-TYPE                                7
D95V9, multiclass
                                  clus
vv                                 DDX42 MUTATED DDX42 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               3
  HEPATOCELLULAR CARCINOMA                     6             357
  HEPATOCHOLANGIOCARCINOMA (MIXED)             0               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DDX42 MUTATED     6   0   0   0
  DDX42 WILD-TYPE 321  16   1  22
D95V10, multiclass
    clus
vv   DDX42 MUTATED DDX42 WILD-TYPE
  R0             6             321
  R1             0              16
  R2             0               1
  RX             0              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDX42 MUTATED                                  0     2
  DDX42 WILD-TYPE                                2   158
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DDX42 MUTATED                           0     4
  DDX42 WILD-TYPE                        17   180
D95V11, multiclass
                                  clus
vv                                 DDX42 MUTATED DDX42 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        2             158
  BLACK OR AFRICAN AMERICAN                    0              17
  WHITE                                        4             180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V12, binary
                 cls
clus                0   1
  DDX42 MUTATED     0   6
  DDX42 WILD-TYPE  18 331
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX42 MUTATED      0    6
  DDX42 WILD-TYPE   18  331
                        clus
vv                       DDX42 MUTATED DDX42 WILD-TYPE
  HISPANIC OR LATINO                 0              18
  NOT HISPANIC OR LATINO             6             331
[1] 2 2
[1] FALSE

Clustering(96) Variable = RHCG MUTATION ANALYSIS
D96V1, survival
                sevent
clus2              0   1
  RHCG MUTATED     1   3
  RHCG WILD-TYPE 236 127
  RHCG MUTATED RHCG WILD-TYPE 
             4            363 
  RHCG MUTATED RHCG WILD-TYPE 
             3            127 
$`RHCG MUTATED`
TCGA-DD-A1EE TCGA-DD-AADU TCGA-ES-A2HT TCGA-G3-A25S 
       11.47        18.21        14.40        13.68 

$`RHCG WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       21.34         9.83        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
        9.14         9.86         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.15        79.73        37.78        83.57        53.33       113.00 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG 
       79.40        66.31        19.79        75.65        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       27.19        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       30.61        33.14        32.52        21.70        30.97        26.37 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30        23.05        22.78         1.45        35.67       114.35 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
       13.48         0.53        11.41        75.65        76.41        55.40 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
       12.53        71.80        12.00        15.42         6.41        53.19 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO 
       69.11         0.30         3.52        58.16        42.81        61.68 
TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV 
       13.64        14.20        59.31        51.35        51.52        50.33 
TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 
       46.82         5.59        47.67         5.62         4.50        18.54 
TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA 
       21.63        42.58        44.22        22.09        40.08        40.54 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG 
       40.83        13.97        40.47        39.52         3.78        37.64 
TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN 
       35.67        35.05        34.49        20.91         0.39        29.52 
TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADW 
       14.89        15.06        14.33        66.67        15.58        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        23.74        15.72        25.08        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        90.48        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.39        80.71        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        60.99        53.69        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       28.08        13.91        13.35         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20        14.04        13.15        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        20.61        19.59         0.62 
TCGA-EP-A3RK TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 
       11.93        60.89        23.97        19.10        27.88        12.03 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.33         0.39        51.06        53.79        28.27 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 
       25.25        22.95        24.46        20.42        17.10        14.70 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       20.78        11.87        14.14        15.78        15.65        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 
       12.23        13.55         0.89        11.64         2.14        11.87 
TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       28.90         1.02         2.20         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       58.88        26.27        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        22.78        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        25.71        23.21        35.87        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  RHCG MUTATED RHCG WILD-TYPE 
         11.47           0.03 
  RHCG MUTATED RHCG WILD-TYPE 
         18.21         120.82 
  RHCG MUTATED RHCG WILD-TYPE 
         14.04          19.99 
[1] "11.5 - 18.2 (14.0)" "0.0 - 120.8 (20.0)"
[1] "hr=" "3.5"
D96V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  RHCG MUTATED         2        1         0          1          0          0
  RHCG WILD-TYPE     172       85         3         63          9          9
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  RHCG MUTATED          0         0         0
  RHCG WILD-TYPE        2         1         2
D96V3, multiclass
            clus
vv           RHCG MUTATED RHCG WILD-TYPE
  STAGE I               2            172
  STAGE II              1             85
  STAGE III             0              3
  STAGE IIIA            1             63
  STAGE IIIB            0              9
  STAGE IIIC            0              9
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RHCG MUTATED     2   1   1   0
  RHCG WILD-TYPE 182  93  78  13
D96V4, multiclass
    clus
vv   RHCG MUTATED RHCG WILD-TYPE
  T1            2            182
  T2            1             93
  T3            1             78
  T4            0             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V5, binary
                cls
clus               0   1
  RHCG MUTATED     3   0
  RHCG WILD-TYPE 251   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHCG MUTATED      3    0
  RHCG WILD-TYPE  251    4
   clus
vv  RHCG MUTATED RHCG WILD-TYPE
  0            3            251
  1            0              4
[1] 2 2
[1] FALSE
D96V6, binary
                cls
clus               0   1
  RHCG MUTATED     3   0
  RHCG WILD-TYPE 266   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHCG MUTATED      3    0
  RHCG WILD-TYPE  266    4
   clus
vv  RHCG MUTATED RHCG WILD-TYPE
  0            3            266
  1            0              4
[1] 2 2
[1] FALSE
D96V7, binary
                cls
clus               0   1
  RHCG MUTATED     0   4
  RHCG WILD-TYPE 121 248
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHCG MUTATED      0    4
  RHCG WILD-TYPE  121  248
        clus
vv       RHCG MUTATED RHCG WILD-TYPE
  FEMALE            0            121
  MALE              4            248
[1] 2 2
[1] FALSE
D96V8, binary
                cls
clus               0   1
  RHCG MUTATED     3   0
  RHCG WILD-TYPE 338   9
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHCG MUTATED      3    0
  RHCG WILD-TYPE  338    9
     clus
vv    RHCG MUTATED RHCG WILD-TYPE
  NO             3            338
  YES            0              9
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  RHCG MUTATED                         0                        4
  RHCG WILD-TYPE                       3                      359
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  RHCG MUTATED                                  0
  RHCG WILD-TYPE                                7
D96V9, multiclass
                                  clus
vv                                 RHCG MUTATED RHCG WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              3
  HEPATOCELLULAR CARCINOMA                    4            359
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RHCG MUTATED     3   1   0   0
  RHCG WILD-TYPE 324  15   1  22
D96V10, multiclass
    clus
vv   RHCG MUTATED RHCG WILD-TYPE
  R0            3            324
  R1            1             15
  R2            0              1
  RX            0             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RHCG MUTATED                                  0     1
  RHCG WILD-TYPE                                2   159
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RHCG MUTATED                           1     2
  RHCG WILD-TYPE                        16   182
D96V11, multiclass
                                  clus
vv                                 RHCG MUTATED RHCG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1            159
  BLACK OR AFRICAN AMERICAN                   1             16
  WHITE                                       2            182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V12, binary
                cls
clus               0   1
  RHCG MUTATED     0   4
  RHCG WILD-TYPE  18 333
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHCG MUTATED      0    4
  RHCG WILD-TYPE   18  333
                        clus
vv                       RHCG MUTATED RHCG WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            4            333
[1] 2 2
[1] FALSE

Clustering(97) Variable = SWAP70 MUTATION ANALYSIS
D97V1, survival
                  sevent
clus2                0   1
  SWAP70 MUTATED     1   4
  SWAP70 WILD-TYPE 236 126
  SWAP70 MUTATED SWAP70 WILD-TYPE 
               5              362 
  SWAP70 MUTATED SWAP70 WILD-TYPE 
               4              126 
$`SWAP70 MUTATED`
TCGA-BC-A112 TCGA-2Y-A9H8 TCGA-DD-A3A1 TCGA-ED-A7PZ TCGA-ES-A2HT 
        5.03        20.81         7.66         0.20        14.40 

$`SWAP70 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A5W4 
       83.24        11.74        38.40         8.61        69.57        17.98 
TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV TCGA-DD-AAE7 
       36.66         0.36        90.28        26.83        18.87        21.17 
TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A3I1 
       21.83        18.90        23.64         9.96        22.62         8.12 
TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC TCGA-G3-A7M9 
        6.38        81.73        30.74        22.13        22.06         1.84 
TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H TCGA-T1-A6J8 
       20.75         2.14        31.27        12.72        24.56         0.76 
TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 TCGA-ZS-A9CE 
        7.04        10.32        44.02        29.52         0.69        40.80 
TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX TCGA-2Y-A9GY 
       23.80        53.39        63.75        41.79        80.28        24.89 
TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 TCGA-2Y-A9H4 
       27.88       120.82        40.41        56.91        49.84        47.74 
TCGA-2Y-A9H5 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB TCGA-3K-AAZ8 TCGA-5C-A9VG 
       18.25        22.92         1.18         8.55        13.02        10.78 
TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D TCGA-5R-AAAM TCGA-BC-4073 
       10.59         0.66        17.10        14.76         1.51        27.91 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG 
       23.38         1.12        44.42        45.93         0.26        22.36 
TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       14.60        18.48        44.81        13.45         0.66         4.24 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 
        8.22         2.86         3.19         3.39         4.24         3.35 
TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        7.20         3.32         9.86         9.96        10.36        11.93 
TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.41         9.99         8.94         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS 
       12.00        13.12        12.56         8.61         9.14         9.86 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       19.79        75.65        11.47        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W 
        6.02        33.04        18.35        13.64        21.14        27.19 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A2 TCGA-DD-A3A3 
       55.69         5.62        19.76        25.81        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       20.12       102.74       107.11        13.78        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ 
       32.52        21.70        30.97        26.37        30.15        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        23.93         9.30        23.05 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 
       22.78         1.45        35.67       114.35        13.48         0.53 
TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE 
       11.41        75.65        76.41        55.40        12.53        71.80 
TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK 
       12.00        15.42         6.41        53.19        69.11         0.30 
TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ 
        3.52        58.16        42.81        61.68        13.64        14.20 
TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX 
       59.31        51.35        51.52        50.33        46.82         5.59 
TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 
       47.67         5.62         4.50        18.54        21.63        42.58 
TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC 
       44.22        22.09        40.08        40.54        40.83        13.97 
TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ 
       40.47        39.52         3.78        37.64        35.67        35.05 
TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADP 
       34.49        20.91         0.39        29.52        14.89        15.06 
TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW TCGA-DD-AADY 
       14.33        66.67        15.58        18.21        19.30        18.25 
TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE6 
       18.25        18.15        20.98        18.61        19.99         4.64 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAEI 
       23.74        15.72        25.08        26.63        25.78        50.33 
TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
       35.08        90.48        89.69        82.62        59.93        72.39 
TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 
       80.71        76.18        56.48        64.77        62.47        66.25 
TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
       65.39        60.99        53.69        29.92        26.93        28.08 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO 
       13.91        13.35         9.73         0.20        12.82        14.04 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J 
       13.15        13.41        13.35         1.84         0.20        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A23B 
       19.99        20.61        19.59         0.62        11.93        60.89 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       23.97        19.10        27.88        12.03         0.03         0.33 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        0.39        13.68        51.06        53.79        28.27        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        25.25 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 
       22.95        24.46        20.42        17.10        14.70        20.78 
TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 
       11.87        14.14        15.78        15.65        11.80        12.23 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU 
       13.55         0.89        11.64         2.14        11.87        28.90 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.20         2.99        37.71        17.06        16.83 
TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
       11.80        27.25        29.79        13.97        12.03         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO TCGA-NI-A4U2 
       16.67        22.95        20.71         7.53        10.85        58.88 
TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 TCGA-RC-A6M5 
       26.27        17.69        21.01         3.09         0.72         0.49 
TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK 
        0.30        21.04        19.33        19.04        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       36.10        27.88        19.76        16.44         1.71        15.98 
TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       10.75        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  SWAP70 MUTATED SWAP70 WILD-TYPE 
            0.20             0.03 
  SWAP70 MUTATED SWAP70 WILD-TYPE 
           20.81           120.82 
  SWAP70 MUTATED SWAP70 WILD-TYPE 
            7.66            19.89 
[1] "0.2 - 20.8 (7.7)"   "0.0 - 120.8 (19.9)"
[1] "hr=" "5.6"
D97V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  SWAP70 MUTATED         1        1         0          1          0          0
  SWAP70 WILD-TYPE     173       85         3         63          9          9
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  SWAP70 MUTATED          0         0         0
  SWAP70 WILD-TYPE        2         1         2
D97V3, multiclass
            clus
vv           SWAP70 MUTATED SWAP70 WILD-TYPE
  STAGE I                 1              173
  STAGE II                1               85
  STAGE III               0                3
  STAGE IIIA              1               63
  STAGE IIIB              0                9
  STAGE IIIC              0                9
  STAGE IV                0                2
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SWAP70 MUTATED     2   1   2   0
  SWAP70 WILD-TYPE 182  93  77  13
D97V4, multiclass
    clus
vv   SWAP70 MUTATED SWAP70 WILD-TYPE
  T1              2              182
  T2              1               93
  T3              2               77
  T4              0               13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V5, binary
                  cls
clus                 0   1
  SWAP70 MUTATED     1   0
  SWAP70 WILD-TYPE 253   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SWAP70 MUTATED      1    0
  SWAP70 WILD-TYPE  253    4
   clus
vv  SWAP70 MUTATED SWAP70 WILD-TYPE
  0              1              253
  1              0                4
[1] 2 2
[1] FALSE
D97V6, binary
                  cls
clus                 0   1
  SWAP70 MUTATED     2   0
  SWAP70 WILD-TYPE 267   4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SWAP70 MUTATED      2    0
  SWAP70 WILD-TYPE  267    4
   clus
vv  SWAP70 MUTATED SWAP70 WILD-TYPE
  0              2              267
  1              0                4
[1] 2 2
[1] FALSE
D97V7, binary
                  cls
clus                 0   1
  SWAP70 MUTATED     1   4
  SWAP70 WILD-TYPE 120 248
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SWAP70 MUTATED      1    4
  SWAP70 WILD-TYPE  120  248
        clus
vv       SWAP70 MUTATED SWAP70 WILD-TYPE
  FEMALE              1              120
  MALE                4              248
[1] 2 2
[1] FALSE
D97V8, binary
                  cls
clus                 0   1
  SWAP70 MUTATED     4   0
  SWAP70 WILD-TYPE 337   9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SWAP70 MUTATED      4    0
  SWAP70 WILD-TYPE  337    9
     clus
vv    SWAP70 MUTATED SWAP70 WILD-TYPE
  NO               4              337
  YES              0                9
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  SWAP70 MUTATED                         0                        5
  SWAP70 WILD-TYPE                       3                      358
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  SWAP70 MUTATED                                  0
  SWAP70 WILD-TYPE                                7
D97V9, multiclass
                                  clus
vv                                 SWAP70 MUTATED SWAP70 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                3
  HEPATOCELLULAR CARCINOMA                      5              358
  HEPATOCHOLANGIOCARCINOMA (MIXED)              0                7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SWAP70 MUTATED     5   0   0   0
  SWAP70 WILD-TYPE 322  16   1  22
D97V10, multiclass
    clus
vv   SWAP70 MUTATED SWAP70 WILD-TYPE
  R0              5              322
  R1              0               16
  R2              0                1
  RX              0               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SWAP70 MUTATED                                  0     1
  SWAP70 WILD-TYPE                                2   159
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SWAP70 MUTATED                           1     2
  SWAP70 WILD-TYPE                        16   182
D97V11, multiclass
                                  clus
vv                                 SWAP70 MUTATED SWAP70 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         1              159
  BLACK OR AFRICAN AMERICAN                     1               16
  WHITE                                         2              182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V12, binary
                  cls
clus                 0   1
  SWAP70 MUTATED     0   4
  SWAP70 WILD-TYPE  18 333
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SWAP70 MUTATED      0    4
  SWAP70 WILD-TYPE   18  333
                        clus
vv                       SWAP70 MUTATED SWAP70 WILD-TYPE
  HISPANIC OR LATINO                  0               18
  NOT HISPANIC OR LATINO              4              333
[1] 2 2
[1] FALSE

Clustering(98) Variable = BIN1 MUTATION ANALYSIS
D98V1, survival
                sevent
clus2              0   1
  BIN1 MUTATED     2   2
  BIN1 WILD-TYPE 235 128
  BIN1 MUTATED BIN1 WILD-TYPE 
             4            363 
  BIN1 MUTATED BIN1 WILD-TYPE 
             2            128 
$`BIN1 MUTATED`
TCGA-DD-A116 TCGA-DD-A73G TCGA-G3-A3CJ TCGA-GJ-A9DB 
       53.33       114.35        19.53         2.20 

$`BIN1 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
        1.51        27.91        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32        23.38         1.12        44.42        45.93 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP 
        0.26        22.36        14.60        18.48        44.81        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         4.24         8.22         2.86         3.19         3.39 
TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        4.24         3.35         7.20         3.32         9.86         9.96 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A5UE TCGA-CC-A7IE 
       10.36        11.93        11.41         9.99         8.94         7.13 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
       21.34         9.83        12.00        13.12        12.56         8.61 
TCGA-CC-A7IL TCGA-CC-A8HS TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS 
        9.14         9.86         4.60        11.31         9.17         6.94 
TCGA-CC-A9FW TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 
        8.15        79.73        37.78        83.57       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG 
       66.31        19.79        75.65        11.47        12.95        45.11 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
       49.15         6.02        33.04        18.35        13.64        21.14 
TCGA-DD-A39W TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       27.19        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       30.61        33.14        32.52        21.70        30.97        26.37 
TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       30.15        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        23.93 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AA3A 
        9.30        23.05        22.78         1.45        35.67        13.48 
TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD 
        0.53        11.41        75.65        76.41        55.40        12.53 
TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ 
       71.80        12.00        15.42         6.41        53.19        69.11 
TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP 
        0.30         3.52        58.16        42.81        61.68        13.64 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW 
       14.20        59.31        51.35        51.52        50.33        46.82 
TCGA-DD-AACX TCGA-DD-AACY TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 
        5.59        47.67         5.62         4.50        18.54        21.63 
TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB 
       42.58        44.22        22.09        40.08        40.54        40.83 
TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI 
       13.97        40.47        39.52         3.78        37.64        35.67 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
       35.05        34.49        20.91         0.39        29.52        14.89 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
       15.06        14.33        66.67        15.58        18.21        19.30 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
       18.25        18.25        18.15        20.98        18.61        19.99 
TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEH 
        4.64        23.74        15.72        25.08        26.63        25.78 
TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS 
       50.33        35.08        90.48        89.69        82.62        59.93 
TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY TCGA-DD-AAVZ 
       72.39        80.71        76.18        56.48        64.77        62.47 
TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 TCGA-ED-A4XI 
       66.25        65.39        60.99        53.69        29.92        26.93 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       28.08        13.91        13.35         9.73         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20        14.04        13.15        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        20.61        19.59         0.62 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        14.86        21.53        25.64         5.92 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        25.25        22.95        24.46        20.42        17.10 
TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ TCGA-G3-AAV0 
       14.70        20.78        11.87        14.14        15.78        15.65 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 TCGA-G3-AAV6 
       11.80        12.23        13.55         0.89        11.64         2.14 
TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG 
       11.87        28.90         1.02         2.99        37.71        17.06 
TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A9QC TCGA-LG-A9QD 
       16.83        11.80        27.25        29.79        13.97        12.03 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A520 TCGA-MR-A8JO 
        9.57        16.67        22.95        20.71         7.53        10.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A6M4 
       58.88        26.27        17.69        21.01         3.09         0.72 
TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF TCGA-RC-A7SH 
        0.49         0.30        21.04        19.33        19.04        15.39 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        36.10        27.88        19.76        16.44         1.71 
TCGA-UB-A7ME TCGA-UB-AA0U TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 
       15.98        10.75        11.34         0.99        12.99        20.22 
TCGA-WX-AA46 TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 
       24.85        18.28        33.86        30.41        22.78        13.55 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 
       35.77        25.71        23.21        35.87        25.15        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CF TCGA-ZS-A9CG 
       45.57        79.30        11.21 

  BIN1 MUTATED BIN1 WILD-TYPE 
          2.20           0.03 
  BIN1 MUTATED BIN1 WILD-TYPE 
        114.35         120.82 
  BIN1 MUTATED BIN1 WILD-TYPE 
         36.43          19.76 
[1] "2.2 - 114.3 (36.4)" "0.0 - 120.8 (19.8)"
[1] "hr=" "1.3"
D98V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  BIN1 MUTATED         2        1         0          1          0          0
  BIN1 WILD-TYPE     172       85         3         63          9          9
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  BIN1 MUTATED          0         0         0
  BIN1 WILD-TYPE        2         1         2
D98V3, multiclass
            clus
vv           BIN1 MUTATED BIN1 WILD-TYPE
  STAGE I               2            172
  STAGE II              1             85
  STAGE III             0              3
  STAGE IIIA            1             63
  STAGE IIIB            0              9
  STAGE IIIC            0              9
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BIN1 MUTATED     2   1   1   0
  BIN1 WILD-TYPE 182  93  78  13
D98V4, multiclass
    clus
vv   BIN1 MUTATED BIN1 WILD-TYPE
  T1            2            182
  T2            1             93
  T3            1             78
  T4            0             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V5, binary
                cls
clus               0   1
  BIN1 MUTATED     4   0
  BIN1 WILD-TYPE 250   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  BIN1 MUTATED      4    0
  BIN1 WILD-TYPE  250    4
   clus
vv  BIN1 MUTATED BIN1 WILD-TYPE
  0            4            250
  1            0              4
[1] 2 2
[1] FALSE
D98V6, binary
                cls
clus               0   1
  BIN1 MUTATED     3   0
  BIN1 WILD-TYPE 266   4
[1] "tbl2"
                cls
clus             [,1] [,2]
  BIN1 MUTATED      3    0
  BIN1 WILD-TYPE  266    4
   clus
vv  BIN1 MUTATED BIN1 WILD-TYPE
  0            3            266
  1            0              4
[1] 2 2
[1] FALSE
D98V7, binary
                cls
clus               0   1
  BIN1 MUTATED     1   3
  BIN1 WILD-TYPE 120 249
[1] "tbl2"
                cls
clus             [,1] [,2]
  BIN1 MUTATED      1    3
  BIN1 WILD-TYPE  120  249
        clus
vv       BIN1 MUTATED BIN1 WILD-TYPE
  FEMALE            1            120
  MALE              3            249
[1] 2 2
[1] FALSE
D98V8, binary
                cls
clus               0   1
  BIN1 MUTATED     3   1
  BIN1 WILD-TYPE 338   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  BIN1 MUTATED      3    1
  BIN1 WILD-TYPE  338    8
     clus
vv    BIN1 MUTATED BIN1 WILD-TYPE
  NO             3            338
  YES            1              8
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  BIN1 MUTATED                         0                        4
  BIN1 WILD-TYPE                       3                      359
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  BIN1 MUTATED                                  0
  BIN1 WILD-TYPE                                7
D98V9, multiclass
                                  clus
vv                                 BIN1 MUTATED BIN1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              3
  HEPATOCELLULAR CARCINOMA                    4            359
  HEPATOCHOLANGIOCARCINOMA (MIXED)            0              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BIN1 MUTATED     4   0   0   0
  BIN1 WILD-TYPE 323  16   1  22
D98V10, multiclass
    clus
vv   BIN1 MUTATED BIN1 WILD-TYPE
  R0            4            323
  R1            0             16
  R2            0              1
  RX            0             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BIN1 MUTATED                                  1     1
  BIN1 WILD-TYPE                                1   159
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BIN1 MUTATED                           0     2
  BIN1 WILD-TYPE                        17   182
D98V11, multiclass
                                  clus
vv                                 BIN1 MUTATED BIN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              1
  ASIAN                                       1            159
  BLACK OR AFRICAN AMERICAN                   0             17
  WHITE                                       2            182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V12, binary
                cls
clus               0   1
  BIN1 MUTATED     0   4
  BIN1 WILD-TYPE  18 333
[1] "tbl2"
                cls
clus             [,1] [,2]
  BIN1 MUTATED      0    4
  BIN1 WILD-TYPE   18  333
                        clus
vv                       BIN1 MUTATED BIN1 WILD-TYPE
  HISPANIC OR LATINO                0             18
  NOT HISPANIC OR LATINO            4            333
[1] 2 2
[1] FALSE

Clustering(99) Variable = SMARCA4 MUTATION ANALYSIS
D99V1, survival
                   sevent
clus2                 0   1
  SMARCA4 MUTATED     5   6
  SMARCA4 WILD-TYPE 232 124
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               11               356 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
                6               124 
$`SMARCA4 MUTATED`
TCGA-BC-A10R TCGA-CC-A5UE TCGA-DD-A1EF TCGA-DD-A3A0 TCGA-DD-AACZ TCGA-DD-AADN 
       10.13         8.94        12.95        25.81         5.62        29.52 
TCGA-DD-AADQ TCGA-ED-A66Y TCGA-MI-A75G TCGA-UB-A7MB TCGA-UB-AA0U 
       14.33         9.73        22.95        19.76        10.75 

$`SMARCA4 WILD-TYPE`
TCGA-2Y-A9GV TCGA-2Y-A9H6 TCGA-2Y-A9H7 TCGA-4R-AA8I TCGA-BC-A110 TCGA-BC-A112 
       83.24        11.74        38.40         8.61        69.57         5.03 
TCGA-BC-A5W4 TCGA-BD-A3ER TCGA-DD-A3A8 TCGA-DD-A4ND TCGA-DD-A4NI TCGA-DD-AADV 
       17.98        36.66         0.36        90.28        26.83        18.87 
TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAEA TCGA-DD-AAEG TCGA-EP-A3JL TCGA-ES-A2HS 
       21.17        21.83        18.90        23.64         9.96        22.62 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A4ZP TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A6UC 
        8.12         6.38        81.73        30.74        22.13        22.06 
TCGA-G3-A7M9 TCGA-K7-A5RF TCGA-KR-A7K0 TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75H 
        1.84        20.75         2.14        31.27        12.72        24.56 
TCGA-T1-A6J8 TCGA-UB-A7MF TCGA-UB-AA0V TCGA-XR-A8TC TCGA-XR-A8TG TCGA-ZP-A9D1 
        0.76         7.04        10.32        44.02        29.52         0.69 
TCGA-ZS-A9CE TCGA-2Y-A9GS TCGA-2Y-A9GT TCGA-2Y-A9GU TCGA-2Y-A9GW TCGA-2Y-A9GX 
       40.80        23.80        53.39        63.75        41.79        80.28 
TCGA-2Y-A9GY TCGA-2Y-A9GZ TCGA-2Y-A9H0 TCGA-2Y-A9H1 TCGA-2Y-A9H2 TCGA-2Y-A9H3 
       24.89        27.88       120.82        40.41        56.91        49.84 
TCGA-2Y-A9H4 TCGA-2Y-A9H5 TCGA-2Y-A9H8 TCGA-2Y-A9H9 TCGA-2Y-A9HA TCGA-2Y-A9HB 
       47.74        18.25        20.81        22.92         1.18         8.55 
TCGA-3K-AAZ8 TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-5R-AA1C TCGA-5R-AA1D 
       13.02        10.78        10.59         0.66        17.10        14.76 
TCGA-5R-AAAM TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
        1.51        27.91        37.32        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       25.32        23.38         1.12        44.42        45.93         0.26 
TCGA-BC-A3KG TCGA-BC-A69H TCGA-BC-A8YO TCGA-BD-A2L6 TCGA-BD-A3EP TCGA-BW-A5NO 
       22.36        14.60        18.48        44.81        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        4.24         8.22         2.86         3.19         3.39         4.24 
TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
        3.35         7.20         3.32         9.86         9.96        10.36 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UD TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
       11.93        11.41         9.99         7.13        21.34         9.83 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS 
       12.00        13.12        12.56         8.61         9.14         9.86 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FS TCGA-CC-A9FW TCGA-DD-A113 
        4.60        11.31         9.17         6.94         8.15        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        11.47        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39W TCGA-DD-A39X 
       33.04        18.35        13.64        21.14        27.19        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
        5.62        19.76         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      102.74       107.11        13.78        30.61        33.14        32.52 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK 
       21.70        30.97        26.37        30.15        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        23.93         9.30        23.05        22.78 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 
        1.45        35.67       114.35        13.48         0.53        11.41 
TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       75.65        76.41        55.40        12.53        71.80        12.00 
TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL 
       15.42         6.41        53.19        69.11         0.30         3.52 
TCGA-DD-AACM TCGA-DD-AACN TCGA-DD-AACO TCGA-DD-AACP TCGA-DD-AACQ TCGA-DD-AACS 
       58.16        42.81        61.68        13.64        14.20        59.31 
TCGA-DD-AACT TCGA-DD-AACU TCGA-DD-AACV TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACY 
       51.35        51.52        50.33        46.82         5.59        47.67 
TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 
        4.50        18.54        21.63        42.58        44.22        22.09 
TCGA-DD-AAD8 TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADE 
       40.08        40.54        40.83        13.97        40.47        39.52 
TCGA-DD-AADF TCGA-DD-AADG TCGA-DD-AADI TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL 
        3.78        37.64        35.67        35.05        34.49        20.91 
TCGA-DD-AADM TCGA-DD-AADO TCGA-DD-AADP TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
        0.39        14.89        15.06        66.67        15.58        18.21 
TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 
       19.30        18.25        18.25        18.15        20.98        18.61 
TCGA-DD-AAE4 TCGA-DD-AAE6 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEE 
       19.99         4.64        23.74        15.72        25.08        26.63 
TCGA-DD-AAEH TCGA-DD-AAEI TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVQ TCGA-DD-AAVR 
       25.78        50.33        35.08        90.48        89.69        82.62 
TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVV TCGA-DD-AAVW TCGA-DD-AAVX TCGA-DD-AAVY 
       59.93        72.39        80.71        76.18        56.48        64.77 
TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW1 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
       62.47        66.25        65.39        60.99        53.69        29.92 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY 
       26.93        28.08        13.91        13.35         0.20        12.82 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.20        14.04        13.15        13.41        13.35         1.84 
TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
        0.20        18.74        19.99        20.61        19.59         0.62 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       11.93        14.40        60.89        23.97        19.10        27.88 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
       12.03         0.03         0.33         0.39        13.68        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       53.79        28.27        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       19.53        19.23        25.25        22.95        24.46        20.42 
TCGA-G3-A5SM TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-AAUZ 
       17.10        14.70        20.78        11.87        14.14        15.78 
TCGA-G3-AAV0 TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV5 
       15.65        11.80        12.23        13.55         0.89        11.64 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A3OU TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ 
        2.14        11.87        28.90         1.02         2.20         2.99 
TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-K7-AAU7 TCGA-KR-A7K2 TCGA-KR-A7K8 
       37.71        17.06        16.83        11.80        27.25        29.79 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75I TCGA-MR-A520 
       13.97        12.03         9.57        16.67        20.71         7.53 
TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 
       10.85        58.88        26.27        17.69        21.01         3.09 
TCGA-RC-A6M4 TCGA-RC-A6M5 TCGA-RC-A6M6 TCGA-RC-A7S9 TCGA-RC-A7SB TCGA-RC-A7SF 
        0.72         0.49         0.30        21.04        19.33        19.04 
TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD 
       15.39        15.52        36.10        27.88        16.44         1.71 
TCGA-UB-A7ME TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-WX-AA44 TCGA-WX-AA46 
       15.98        11.34         0.99        12.99        20.22        24.85 
TCGA-WX-AA47 TCGA-XR-A8TD TCGA-XR-A8TE TCGA-XR-A8TF TCGA-YA-A8S7 TCGA-ZP-A9CV 
       18.28        33.86        30.41        22.78        13.55        35.77 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZP-A9D4 TCGA-ZS-A9CD 
       25.71        23.21        35.87        25.15        12.99        45.57 
TCGA-ZS-A9CF TCGA-ZS-A9CG 
       79.30        11.21 

  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
             5.62              0.03 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
            29.52            120.82 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
            12.95             19.99 
[1] "5.6 - 29.5 (12.9)"  "0.0 - 120.8 (20.0)"
[1] "hr=" "2.4"
D99V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  SMARCA4 MUTATED         4        4         0          1          1          0
  SMARCA4 WILD-TYPE     170       82         3         63          8          9
                   vv
clus                STAGE IV STAGE IVA STAGE IVB
  SMARCA4 MUTATED          0         0         0
  SMARCA4 WILD-TYPE        2         1         2
D99V3, multiclass
            clus
vv           SMARCA4 MUTATED SMARCA4 WILD-TYPE
  STAGE I                  4               170
  STAGE II                 4                82
  STAGE III                0                 3
  STAGE IIIA               1                63
  STAGE IIIB               1                 8
  STAGE IIIC               0                 9
  STAGE IV                 0                 2
  STAGE IVA                0                 1
  STAGE IVB                0                 2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SMARCA4 MUTATED     4   4   2   1
  SMARCA4 WILD-TYPE 180  90  77  12
D99V4, multiclass
    clus
vv   SMARCA4 MUTATED SMARCA4 WILD-TYPE
  T1               4               180
  T2               4                90
  T3               2                77
  T4               1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V5, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED     6   0
  SMARCA4 WILD-TYPE 248   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED      6    0
  SMARCA4 WILD-TYPE  248    4
   clus
vv  SMARCA4 MUTATED SMARCA4 WILD-TYPE
  0               6               248
  1               0                 4
[1] 2 2
[1] FALSE
D99V6, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED     7   0
  SMARCA4 WILD-TYPE 262   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED      7    0
  SMARCA4 WILD-TYPE  262    4
   clus
vv  SMARCA4 MUTATED SMARCA4 WILD-TYPE
  0               7               262
  1               0                 4
[1] 2 2
[1] FALSE
D99V7, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED     4   7
  SMARCA4 WILD-TYPE 117 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED      4    7
  SMARCA4 WILD-TYPE  117  245
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  FEMALE               4               117
  MALE                 7               245
[1] 2 2
[1] FALSE
D99V8, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED    10   0
  SMARCA4 WILD-TYPE 331   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED     10    0
  SMARCA4 WILD-TYPE  331    9
     clus
vv    SMARCA4 MUTATED SMARCA4 WILD-TYPE
  NO               10               331
  YES               0                 9
[1] 2 2
[1] FALSE
                   vv
clus                FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  SMARCA4 MUTATED                         0                       11
  SMARCA4 WILD-TYPE                       3                      352
                   vv
clus                HEPATOCHOLANGIOCARCINOMA (MIXED)
  SMARCA4 MUTATED                                  0
  SMARCA4 WILD-TYPE                                7
D99V9, multiclass
                                  clus
vv                                 SMARCA4 MUTATED SMARCA4 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                        0                 3
  HEPATOCELLULAR CARCINOMA                      11               352
  HEPATOCHOLANGIOCARCINOMA (MIXED)               0                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SMARCA4 MUTATED    10   1   0   0
  SMARCA4 WILD-TYPE 317  15   1  22
D99V10, multiclass
    clus
vv   SMARCA4 MUTATED SMARCA4 WILD-TYPE
  R0              10               317
  R1               1                15
  R2               0                 1
  RX               0                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMARCA4 MUTATED                                  0     5
  SMARCA4 WILD-TYPE                                2   155
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SMARCA4 MUTATED                           0     6
  SMARCA4 WILD-TYPE                        17   178
D99V11, multiclass
                                  clus
vv                                 SMARCA4 MUTATED SMARCA4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          5               155
  BLACK OR AFRICAN AMERICAN                      0                17
  WHITE                                          6               178
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V12, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED     0  11
  SMARCA4 WILD-TYPE  18 326
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED      0   11
  SMARCA4 WILD-TYPE   18  326
                        clus
vv                       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO              11               326
[1] 2 2
[1] FALSE
